Cryo-EM structure of the yeast fatty acid synthase at 1.9 angstrom resolution
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 8prw
Q-score: 0.712
Singh K, Bunzel G, Graf B, Yip KM, Neumann-Schaal M, Stark H, Chari A
Cell (2023) 186 pp. 5054-5067.e16 [ Pubmed: 37949058 DOI: doi:10.1016/j.cell.2023.10.009 ]
- Fatty acid synthase subunit beta (229 kDa, Protein from Saccharomyces cerevisiae)
- Nadp nicotinamide-adenine-dinucleotide phosphate (743 Da, Ligand)
- Water (18 Da, Ligand)
- Coenzyme a (767 Da, Ligand)
- Fatty acid synthase subunit alpha (207 kDa, Protein from Saccharomyces cerevisiae)
- Yeast fatty acid synthase (Complex from Saccharomyces cerevisiae)
- 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2h-benzo[g]pteridin-1-id-10(5h)-yl)-5-o-phosphonato-d-ribitol (458 Da, Ligand)
Inner spoke ring of the yeast NPC
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 8tj5
Q-score: 0.113
Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP
Mol Cell (2023) 83 pp. 3283-3302.e5 [ Pubmed: 37738963 DOI: doi:10.1016/j.molcel.2023.08.025 ]
- Nuclear pore complex (18 MDa, Complex from Saccharomyces cerevisiae)
- Nucleoporin nup57 (57 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup192 (191 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup188 (188 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup53 (52 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nsp1 (86 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup170 (169 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nic96 (96 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup157 (156 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin 59 (58 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup49/nsp49 (49 kDa, Protein from Saccharomyces cerevisiae)
- Spoke connector (3 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae CMGE dimer nucleating origin DNA melting
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7z13
Q-score: 0.471
Lewis JS, Gross MH, Sousa J, Henrikus SS, Greiwe JF, Nans A, Diffley JFX, Costa A
Nature (2022) 606 pp. 1007-1014 [ Pubmed: 35705812 DOI: doi:10.1038/s41586-022-04829-4 ]
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna helicase (86 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (75 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (25 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- S. cerevisiae cmge dimer nucleating origin dna melting (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Dna (53-mer) (16 kDa, DNA from DNA molecule)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna (53-mer) (16 kDa, DNA from DNA molecule)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7obr
Q-score: 0.492
Jomaa A, Eitzinger S, Zhu Z, Chandrasekar S, Kobayashi K, Shan SO, Ban N
Cell Rep (2021) 36 pp. 109350-109350 [ DOI: doi:10.1016/j.celrep.2021.109350 Pubmed: 34260909 ]
- 60s ribosomal protein l30 (10 kDa, Protein from Rabbit)
- Ribosomal protein l23 (14 kDa, Protein from Rabbit)
- El43 (10 kDa, Protein from Rabbit)
- Srp rna (80 kDa, RNA from dog)
- 60s ribosomal protein l6 (28 kDa, Protein from Rabbit)
- 60s ribosomal protein l27 (15 kDa, Protein from Rabbit)
- 60s ribosomal protein l36 (11 kDa, Protein from Rabbit)
- Ul22 (17 kDa, Protein from Rabbit)
- 60s ribosomal protein l29 (24 kDa, Protein from Rabbit)
- 60s ribosomal protein l7a (36 kDa, Protein from Rabbit)
- El39 (6 kDa, Protein from Rabbit)
- Ul30 (26 kDa, Protein from Rabbit)
- 28s rrna (1 MDa, RNA from rabbit)
- Rnc-srp complex (Complex from Canis lupus familiaris)
- 60s ribosomal protein l4 (46 kDa, Protein from Rabbit)
- 60s ribosomal protein l14 (23 kDa, Protein from Rabbit)
- El18 (21 kDa, Protein from Rabbit)
- Ribosomal protein l24 (7 kDa, Protein from Rabbit)
- El32 (18 kDa, Protein from Rabbit)
- El33 (12 kDa, Protein from Rabbit)
- Signal recognition particle 9 kda protein (10 kDa, Protein from Dog, Canis familiaris)
- Signal recognition particle subunit srp72 (74 kDa, Protein from Dog, Canis familiaris)
- El28 (15 kDa, Protein from Rabbit)
- Ul15 (16 kDa, Protein from Rabbit)
- El21 (18 kDa, Protein from Rabbit)
- 60s ribosomal protein l41 (3 kDa, Protein from Rabbit)
- 60s ribosomal protein l13a (23 kDa, Protein from Rabbit)
- 60s ribosomal protein l18a (20 kDa, Protein from Rabbit)
- Ribosomal protein l37 (11 kDa, Protein from Rabbit)
- Ribosomal protein l11 (20 kDa, Protein from Rabbit)
- 60s ribosomal protein el40 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein el19 (21 kDa, Protein from Oryctolagus cuniculus)
- Ul23 (17 kDa, Protein from Rabbit)
- Ul29 (14 kDa, Protein from Rabbit)
- Signal recognition particle 14 kda protein (12 kDa, Protein from Dog)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l10 (24 kDa, Protein from Rabbit)
- 60s ribosomal protein l8 (26 kDa, Protein from Rabbit)
- Ribosomal protein l26 (17 kDa, Protein from Rabbit)
- Dipeptidyl aminopeptidase b (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Signal recognition particle 54 kda protein (55 kDa, Protein from Dog)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Signal recognition particle 19 (16 kDa, Protein from Dog, Canis familiaris)
- Ribosomal protein l15 (24 kDa, Protein from Rabbit)
- Rnc-srp complex (Complex from Oryctolagus cuniculus)
- Ribosomal protein l22 (11 kDa, Protein from Rabbit)
- 5.8s ribosomal rna (50 kDa, RNA from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l9 (21 kDa, Protein from Rabbit)
- Ul3 (45 kDa, Protein from Rabbit)
- El38 (8 kDa, Protein from rabbit)
- 60s ribosomal protein l34 (14 kDa, Protein from Rabbit)
- 5s ribosomal rna (38 kDa, RNA from Oryctolagus cuniculus)
- Polypeptide nascent chain (Complex from Saccharomyces cerevisiae)
- El42 (12 kDa, Protein from Rabbit)
- El31 (14 kDa, Protein from Rabbit)
- 60s ribosomal protein l5 (34 kDa, Protein from Rabbit)
- Rnc-srp complex (Complex)
- 60s ribosomal protein l13 (24 kDa, Protein from Rabbit)
- Signal recognition particle subunit srp68 (70 kDa, Protein from Dog, Canis familiaris)
Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound, composite map
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7b9v
Q-score: 0.378
Wilkinson ME, Fica SM, Galej WP, Nagai K
Mol Cell (2021) 81 pp. 1439- [ Pubmed: 33705709 DOI: doi:10.1016/j.molcel.2021.02.021 ]
- Clf1 isoform 1 (82 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Baker's yeast)
- 5' exon of ubc4 mrna (15 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- Syf1 isoform 1 (100 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Baker's yeast)
- Bj4_g0054360.mrna.1.cds.1 (50 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- Hlj1_g0053790.mrna.1.cds.1 (27 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
- D-chiro inositol hexakisphosphate (660 Da, Ligand)
- Snt309 isoform 1 (20 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor isy1 (27 kDa, Protein from Baker's yeast)
- Potassium ion (39 Da, Ligand)
- Branched intron and 3' exon of ubc4 pre-mrna (30 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- Cwc22 isoform 1 (67 kDa, Protein from Baker's yeast)
- Bj4_g0027490.mrna.1.cds.1 (12 kDa, Protein from Baker's yeast)
- Ntc20 isoform 1 (15 kDa, Protein from Baker's yeast)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- Splicing factor yju2 (33 kDa, Protein from Baker's yeast)
- Cdc40 isoform 1 (52 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- Y55_g0042700.mrna.1.cds.1 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor atp-dependent rna helicase prp16 (121 kDa, Protein from Baker's yeast)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Unassigned structure (20 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- Bud31 isoform 1 (18 kDa, Protein from Baker's yeast)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Yeast c complex spliceosome with prp18/slu7 bound (2 MDa, Complex from Saccharomyces cerevisiae)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 6xzb
Q-score: 0.432
Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL
RNA (2020) 26 pp. 715-723 [ Pubmed: 32144191 DOI: doi:10.1261/rna.073817.119 ]
- E. coli 70s ribosome (Complex from Escherichia coli (strain K12))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l10 (14 kDa, Protein from Escherichia coli (strain K12))
- Deacylated trnai(met) (24 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- E. coli 70s ribosome in complex with dirithromycin, fmet-phe-trna(phe) and deacylated trna(imet). (2 MDa, Complex)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli (strain K12))
- Dirithromycin (835 Da, Ligand)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli (strain K12))
- 16s rrna (497 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli (strain K12))
- 5s rrna (38 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- Fmet-phe-trna(phe) (25 kDa, RNA from Saccharomyces cerevisiae)
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s18 (6 kDa, Protein from Escherichia coli (strain K12))
- Fmet-phe-trna(phe) (Complex from Saccharomyces cerevisiae)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (12 kDa, Protein from Escherichia coli (strain K12))
- 23s rrna (939 kDa, RNA from Escherichia coli K-12)
CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6woo
Q-score: 0.487
Wang J, Wang J, Puglisi J, Fernandez IS
To Be Published
- Us14 (6 kDa, Protein from Saccharomyces cerevisiae)
- Es8 (22 kDa, Protein from Saccharomyces cerevisiae)
- Us11 (13 kDa, Protein from Saccharomyces cerevisiae)
- El31 (12 kDa, Protein from Saccharomyces cerevisiae)
- Us12 (15 kDa, Protein from Saccharomyces cerevisiae)
- Ul5 (19 kDa, Protein from Saccharomyces cerevisiae)
- Ul14 (14 kDa, Protein from Saccharomyces cerevisiae)
- El36 (10 kDa, Protein from Saccharomyces cerevisiae)
- Es4 (29 kDa, Protein from Saccharomyces cerevisiae)
- El32 (14 kDa, Protein from Saccharomyces cerevisiae)
- El40 (5 kDa, Protein from Saccharomyces cerevisiae)
- El24 (7 kDa, Protein from Saccharomyces cerevisiae)
- Us10 (12 kDa, Protein from Saccharomyces cerevisiae)
- Us7 (22 kDa, Protein from Saccharomyces cerevisiae)
- El14 (14 kDa, Protein from Saccharomyces cerevisiae)
- El18 (20 kDa, Protein from Saccharomyces cerevisiae)
- El37 (9 kDa, Protein from Saccharomyces cerevisiae)
- El41 (3 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- El42 (11 kDa, Protein from Saccharomyces cerevisiae)
- Es26 (11 kDa, Protein from Saccharomyces cerevisiae)
- Us5 (23 kDa, Protein from Saccharomyces cerevisiae)
- El13 (22 kDa, Protein from Saccharomyces cerevisiae)
- Es19 (15 kDa, Protein from Saccharomyces cerevisiae)
- Ul3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s ribosomal rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- Ul6 (21 kDa, Protein from Saccharomyces cerevisiae)
- Es25 (8 kDa, Protein from Saccharomyces cerevisiae)
- Es24 (15 kDa, Protein from Saccharomyces cerevisiae)
- Es28 (7 kDa, Protein from Saccharomyces cerevisiae)
- Es1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Es10 (11 kDa, Protein from Saccharomyces cerevisiae)
- El29 (6 kDa, Protein from Saccharomyces cerevisiae)
- Es31 (6 kDa, Protein from Saccharomyces cerevisiae)
- Es12 (13 kDa, Protein from Saccharomyces cerevisiae)
- Ul10 (21 kDa, Protein from Saccharomyces cerevisiae)
- Ul13 (22 kDa, Protein from Saccharomyces cerevisiae)
- Us2 (22 kDa, Protein from Saccharomyces cerevisiae)
- Met-trna-imet (24 kDa, RNA from Saccharomyces cerevisiae)
- Methionine (149 Da, Ligand)
- Us8 (14 kDa, Protein from Saccharomyces cerevisiae)
- El34 (13 kDa, Protein from Saccharomyces cerevisiae)
- 5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
- El22 (11 kDa, Protein from Saccharomyces cerevisiae)
- Ul2 (26 kDa, Protein from Saccharomyces cerevisiae)
- Ul29 (13 kDa, Protein from Saccharomyces cerevisiae)
- El27 (15 kDa, Protein from Saccharomyces cerevisiae)
- El33 (11 kDa, Protein from Saccharomyces cerevisiae)
- Us19 (11 kDa, Protein from Saccharomyces cerevisiae)
- L10 (12 kDa, Protein from Saccharomyces cerevisiae)
- Ul15 (16 kDa, Protein from Saccharomyces cerevisiae)
- El43 (9 kDa, Protein from Saccharomyces cerevisiae)
- Ul22 (20 kDa, Protein from Saccharomyces cerevisiae)
- El39 (6 kDa, Protein from Saccharomyces cerevisiae)
- Es21 (9 kDa, Protein from Saccharomyces cerevisiae)
- Us4 (20 kDa, Protein from Saccharomyces cerevisiae)
- Ul24 (14 kDa, Protein from Saccharomyces cerevisiae)
- Es17 (14 kDa, Protein from Saccharomyces cerevisiae)
- El8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Ul16 (24 kDa, Protein from Saccharomyces cerevisiae)
- Mrna (1 kDa, RNA from Saccharomyces cerevisiae)
- El21 (18 kDa, Protein from Saccharomyces cerevisiae)
- 25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
- Us3 (24 kDa, Protein from Saccharomyces cerevisiae)
- El15 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Es27 (8 kDa, Protein from Saccharomyces cerevisiae)
- Us19 (15 kDa, Protein from Saccharomyces cerevisiae)
- Ul1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Ul4 (38 kDa, Protein from Saccharomyces cerevisiae)
- El20 (20 kDa, Protein from Saccharomyces cerevisiae)
- Rack1 (34 kDa, Protein from Saccharomyces cerevisiae)
- Es30 (6 kDa, Protein from Saccharomyces cerevisiae)
- El19 (21 kDa, Protein from Saccharomyces cerevisiae)
- El30 (10 kDa, Protein from Saccharomyces cerevisiae)
- N-carboxy-l-threonine (163 Da, Ligand)
- Us15 (16 kDa, Protein from Saccharomyces cerevisiae)
- Ul18 (33 kDa, Protein from Saccharomyces cerevisiae)
- El6 (19 kDa, Protein from Saccharomyces cerevisiae)
- Es7 (21 kDa, Protein from Saccharomyces cerevisiae)
- Eif5b (67 kDa, Protein from Saccharomyces cerevisiae)
- Ul30 (25 kDa, Protein from Saccharomyces cerevisiae)
- 18s ribosomal rna (578 kDa, RNA from Saccharomyces cerevisiae)
- El38 (8 kDa, Protein from Saccharomyces cerevisiae)
- Us13 (15 kDa, Protein from Saccharomyces cerevisiae)
- 80s ribosome with eif5b, met-trnaimet, mrna, and gdp (Complex from Saccharomyces cerevisiae)
- Us17 (16 kDa, Protein from Saccharomyces cerevisiae)
- Es6 (25 kDa, Protein from Saccharomyces cerevisiae)
- Ul23 (13 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6xiq
Q-score: 0.33
Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Forster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM
PNAS (2020) 117 pp. 22157-22166 [ Pubmed: 32855298 DOI: doi:10.1073/pnas.2005301117 ]
- 40s ribosomal protein s23-a (16 kDa, Protein from Baker's yeast)
- Rpl41a isoform 1 (3 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l21-a (18 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s11-a (17 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l17-a (20 kDa, Protein from Baker's yeast)
- Rps22a isoform 1 (14 kDa, Protein from Baker's yeast)
- Rpp0 isoform 1 (33 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s24-a (15 kDa, Protein from Baker's yeast)
- Rps25a isoform 1 (12 kDa, Protein from Baker's yeast)
- Rpl1a isoform 1 (24 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l7-a (27 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l14-a (15 kDa, Protein from Baker's yeast)
- K63 ubiquitinated ribosome (3 MDa, Complex from Saccharomyces cerevisiae)
- Rps2 isoform 1 (27 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l6-a (20 kDa, Protein from Baker's yeast)
- Rpl4a isoform 1 (39 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l25 (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l15-a (24 kDa, Protein from Baker's yeast)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Baker's yeast)
- Rps15 isoform 1 (16 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l18-a (20 kDa, Protein from Baker's yeast)
- Rps26b isoform 1 (13 kDa, Protein from Baker's yeast)
- Rps1a isoform 1 (28 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s7-a (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s0-a (28 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s19-a (15 kDa, Protein from Baker's yeast)
- Rpl3 isoform 1 (43 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l28 (16 kDa, Protein from Baker's yeast)
- Rps8a isoform 1 (22 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l43-a (10 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l20-a (20 kDa, Protein from Baker's yeast)
- Rpl9a isoform 1 (21 kDa, Protein from Baker's yeast)
- Rpl10 isoform 1 (25 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l33-a (12 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s30-a (7 kDa, Protein from Baker's yeast)
- Rps3 isoform 1 (26 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l2-a (27 kDa, Protein from Baker's yeast)
- 35s ribosomal rna (1 MDa, RNA from Baker's yeast)
- 60s ribosomal protein l37-a (9 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l13-a (22 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s4-a (29 kDa, Protein from Baker's yeast)
- Rpl24a isoform 1 (17 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s17-b (15 kDa, Protein from Baker's yeast)
- Mrna (2 kDa, RNA from Baker's yeast)
- Rpl29 isoform 1 (6 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s14-b (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l16-a (22 kDa, Protein from Baker's yeast)
- 18s ribosomal rna (579 kDa, RNA from Baker's yeast)
- 5.8s ribosomal rna (50 kDa, RNA from Baker's yeast)
- 40s ribosomal protein s18-a (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l34-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l26-a (14 kDa, Protein from Baker's yeast)
- Rps20 isoform 1 (13 kDa, Protein from Baker's yeast)
- Rpl12a isoform 1 (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l19-a (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s21-a (9 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l42-a (12 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l23-a (14 kDa, Protein from Baker's yeast)
- Rpl5 isoform 1 (33 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l31-a (12 kDa, Protein from Baker's yeast)
- Transfer rna (24 kDa, RNA from Baker's yeast)
- Rpl8a isoform 1 (28 kDa, Protein from Baker's yeast)
- Rpl11b isoform 1 (19 kDa, Protein from Baker's yeast)
- Rpl38 isoform 1 (8 kDa, Protein from Baker's yeast)
- Rps5p (25 kDa, Protein from Baker's yeast)
- 5s ribosomal rna (38 kDa, RNA from Baker's yeast)
- 60s ribosomal protein l40 (14 kDa, Protein from Baker's yeast)
- Rpl32 isoform 1 (14 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l39 (6 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l27-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l30 (11 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l35-a (13 kDa, Protein from Baker's yeast)
- Rps29a isoform 1 (6 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s6-a (27 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s10-a (12 kDa, Protein from Baker's yeast)
- Rps28a isoform 1 (7 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l22-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l36-a (11 kDa, Protein from Baker's yeast)
Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6xir
Q-score: 0.405
Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Forster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM
PNAS (2020) 117 pp. 22157-22166 [ DOI: doi:10.1073/pnas.2005301117 Pubmed: 32855298 ]
- Rpl9a isoform 1 (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s19-a (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s6-a (27 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s21-a (9 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l27-a (15 kDa, Protein from Baker's yeast)
- Rps29a isoform 1 (6 kDa, Protein from Baker's yeast)
- Rps1a isoform 1 (28 kDa, Protein from Baker's yeast)
- K63 ubiquitinated ribosome (Complex from Saccharomyces cerevisiae)
- Rpl5 isoform 1 (33 kDa, Protein from Baker's yeast)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Baker's yeast)
- 5.8s ribosomal rna (50 kDa, RNA from Baker's yeast)
- Rpl32 isoform 1 (14 kDa, Protein from Baker's yeast)
- Rpl29 isoform 1 (6 kDa, Protein from Baker's yeast)
- Rpl8a isoform 1 (28 kDa, Protein from Baker's yeast)
- Rps26b isoform 1 (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l7-a (27 kDa, Protein from Baker's yeast)
- Rps3 isoform 1 (26 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l6-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l34-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l21-a (18 kDa, Protein from Baker's yeast)
- 5s ribosomal rna (38 kDa, RNA from Baker's yeast)
- 60s ribosomal protein l30 (11 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l42-a (12 kDa, Protein from Baker's yeast)
- Rps22a isoform 1 (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l14-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l23-a (14 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s14-b (14 kDa, Protein from Baker's yeast)
- Rps15 isoform 1 (16 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l13-a (22 kDa, Protein from Baker's yeast)
- Rpl10 isoform 1 (25 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l36-a (11 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s24-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l26-a (14 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l35-a (13 kDa, Protein from Baker's yeast)
- Rps5p (25 kDa, Protein from Baker's yeast)
- Rps8a isoform 1 (22 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s10-a (12 kDa, Protein from Baker's yeast)
- Rpl41a isoform 1 (3 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l43-a (10 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l37-a (9 kDa, Protein from Baker's yeast)
- Rps28a isoform 1 (7 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l16-a (22 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l33-a (12 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
- 18s ribosomal rna (579 kDa, RNA from Baker's yeast)
- 60s ribosomal protein l25 (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s4-a (29 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s11-a (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l22-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l15-a (24 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l18-a (20 kDa, Protein from Baker's yeast)
- Rpl3 isoform 1 (43 kDa, Protein from Baker's yeast)
- Rps2 isoform 1 (27 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s7-a (21 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Rpl38 isoform 1 (8 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l20-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l17-a (20 kDa, Protein from Baker's yeast)
- Rpl4a isoform 1 (39 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l2-a (27 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s18-a (17 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s23-a (16 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
- Rpl11b isoform 1 (19 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l19-a (21 kDa, Protein from Baker's yeast)
- Rps25a isoform 1 (12 kDa, Protein from Baker's yeast)
- 35s ribosomal rna (1 MDa, RNA from Baker's yeast)
- 60s ribosomal protein l31-a (12 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s0-a (28 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
- Rps20 isoform 1 (13 kDa, Protein from Baker's yeast)
- Rpl24a isoform 1 (17 kDa, Protein from Baker's yeast)
- Transfer rna (24 kDa, RNA from Baker's yeast)
- 60s ribosomal protein l28 (16 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l39 (6 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s17-b (15 kDa, Protein from Baker's yeast)
Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6ylg
Q-score: 0.545
Kater L, Mitterer V, Thoms M, Cheng J, Berninghausen O, Beckmann R, Hurt E
Mol Cell (2020) 79 pp. 615-628.e5 [ Pubmed: 32668200 DOI: doi:10.1016/j.molcel.2020.06.032 ]
- 60s ribosomal protein l5 (33 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l21-a (18 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l16-a (22 kDa, Protein from Baker's yeast)
- Probable metalloprotease arx1 (65 kDa, Protein from Baker's yeast)
- Protein sda1 (86 kDa, Protein from Baker's yeast)
- Rrna-processing protein cgr1 (14 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 5.8s rrna (50 kDa, RNA from Baker's yeast)
- 60s ribosomal protein l3 (43 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein nsa2 (29 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l11-a (19 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l34-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l26-a (14 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l17-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l19-a (21 kDa, Protein from Baker's yeast)
- Bud site selection protein 20 (18 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l28 (16 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l4-a (39 kDa, Protein from Baker's yeast)
- Pre-rrna-processing protein ipi1 (37 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l32 (14 kDa, Protein from Baker's yeast)
- Nuclear gtp-binding protein nug1 (57 kDa, Protein from Baker's yeast)
- Upf0642 protein ybl028c (12 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l12-a (17 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l23-a (14 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein alb1 (19 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l1-a (24 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l43-a (10 kDa, Protein from Baker's yeast)
- Ribosome assembly protein 4 (57 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l20-a (20 kDa, Protein from Baker's yeast)
- Nucleolar gtp-binding protein 1 (74 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l39 (6 kDa, Protein from Baker's yeast)
- Rix1-rea1 pre-60s assembly particle - 60s core portion (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l14-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l27-a (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l31-a (12 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l6-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l33-a (12 kDa, Protein from Baker's yeast)
- Ribosome assembly factor mrt4 (27 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l30 (11 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l9-a (21 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l25 (15 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l15-a (24 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l35-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l38 (8 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l2-a (27 kDa, Protein from Baker's yeast)
- 25s rrna (1 MDa, RNA from Baker's yeast)
- Nucleolar gtp-binding protein 2 (55 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l37-a (9 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l18-a (20 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l13-a (22 kDa, Protein from Baker's yeast)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Baker's yeast)
- 5s rrna (38 kDa, RNA from Baker's yeast)
- 60s ribosomal protein l8-a (28 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l22-a (13 kDa, Protein from Baker's yeast)
- 60s ribosomal protein l36-a (11 kDa, Protein from Baker's yeast)