Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8bf9
Q-score: 0.552
Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V
EMBO Rep (2023) 24 pp. e57910-e57910 [ Pubmed: 37983950 DOI: doi:10.15252/embr.202357910 ]
- Translocon-associated protein subunit alpha (39 kDa, Protein from Ovis aries)
- Ribosomal protein l23/l25 n-terminal domain-containing protein (17 kDa, Protein from Ovis aries)
- Ribosomal protein l37 (11 kDa, Protein from Ovis aries)
- Large ribosomal subunit protein el31 (14 kDa, Protein from Ovis aries)
- Sec61b (2 kDa, Protein from Ovis aries)
- Translocon-associated protein subunit beta (20 kDa, Protein from Ovis aries)
- Large ribosomal subunit protein ul22 (21 kDa, Protein from Ovis aries)
- Rl26 protein (fragment) (15 kDa, Protein from Ovis aries)
- Large ribosomal subunit protein el38 (8 kDa, Protein from Ovis aries)
- Rl22 protein (fragment) (14 kDa, Protein from Ovis aries)
- Ribosomal protein l19 (23 kDa, Protein from Ovis aries)
- Sec61a (52 kDa, Protein from Ovis aries)
- 60s ribosomal protein l39 (6 kDa, Protein from Ovis aries)
- Mammlian ribosome sec61 trap complex (3 MDa, Complex from Ovis aries)
- Translocon-associated protein subunit delta (18 kDa, Protein from Ovis aries)
- Translocon-associated protein subunit gamma (21 kDa, Protein from Ovis aries)
- Protein transport protein sec61 subunit gamma (9 kDa, Protein from Ovis aries)
- Rna (156-mer) (50 kDa, RNA from Ovis aries)
- Rna (1766) (1 MDa, RNA from Ovis aries)
- Large ribosomal subunit protein ul29 (14 kDa, Protein from Ovis aries)
Structure of the TRAP complex with the Sec translocon and a translating ribosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8btk
Q-score: 0.362
Jaskolowski M, Jomaa A, Gamerdinger M, Shrestha S, Leibundgut M, Deuerling E, Ban N
Nat Struct Mol Biol (2023) 30 pp. 770-777 [ Pubmed: 37170030 DOI: doi:10.1038/s41594-023-00990-0 ]
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- El18 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (30 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_s5_c domain-containing protein,40s ribosomal protein s2 (31 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Translocon-associated protein subunit alpha (32 kDa, Protein from Canis lupus familiaris)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- L13 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal large subunit (60s) (Complex from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Spermine (202 Da, Ligand)
- Ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- Signal sequence receptor subunit 3 (21 kDa, Protein from Canis lupus familiaris)
- Spermidine (145 Da, Ligand)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- Es26 (13 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal small subunit (ssu) (Complex from Oryctolagus cuniculus)
- Ul30,60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
- P-site trna (24 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s14 (16 kDa, Protein from Oryctolagus cuniculus)
- Acetylamino-acetic acid (117 Da, Ligand)
- 60s ribosomal protein l22 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (22 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Canis lupus familiaris)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Canis lupus familiaris)
- 60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- P-site trna (Complex from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- Trap complex (Complex from canis lupus familiaris)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- Structure of the trap complex with the sec translocon and a translating ribosome (Complex from Oryctolagus cuniculus)
- Sec61 translocon (Complex from canis lupus familiaris)
- Nascent chain (2 kDa, Protein from Saccharomyces cerevisiae)
- Mrna (1 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s19 (16 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Canis lupus familiaris)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- Translocon-associated protein subunit delta (18 kDa, Protein from Canis lupus familiaris)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- Translocon-associated protein subunit beta (20 kDa, Protein from Canis lupus familiaris)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- El38 (8 kDa, Protein from Oryctolagus cuniculus)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
Cryo-EM structure of the human Sec61 complex in a partially-open apo state (Class 1)
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8dnv
Q-score: 0.519
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- A human-yeast chimeric sec complex (Complex from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human Sec61 complex in a partially-open apo state (Class 2)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8dnw
Q-score: 0.467
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- A human-yeast chimeric sec complex (Complex from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human Sec61 complex inhibited by cotransin
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8dnx
Q-score: 0.465
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- A human-yeast chimeric sec complex treated with cotransin (Complex from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- Cotransin analogue peptide inhibitor (953 Da, Protein from synthetic construct)
Cryo-EM structure of the human Sec61 complex inhibited by decatransin
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8dny
Q-score: 0.546
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- Decatransin peptide inhibitor (1 kDa, Protein from synthetic construct)
- A human-yeast chimeric sec complex treated with decatransin (Complex from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human Sec61 complex inhibited by apratoxin F
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8dnz
Q-score: 0.602
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- Apratoxin f peptide inhibitor (848 Da, Protein from Lyngbya bouillonii)
- A human-yeast chimeric sec complex treated with apratoxin f (Complex from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human Sec61 complex inhibited by mycolactone
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8do0
Q-score: 0.544
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- Water (18 Da, Ligand)
- A human-yeast chimeric sec complex treated with mycolactone (Complex from Homo sapiens)
- [(6~{s},7~{s},9~{z},12~{r})-12-[(~{z},2~{s},6~{r},7~{r},9~{r})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl] (2~{e},4~{e},6~{e},8~{e},10~{e},12~{s},13~{s},15~{s})-4,6,10-trimethyl-12,13,15-tris(oxidanyl)hexadeca-2,4,6,8,10-pentaenoate (743 Da, Ligand)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human Sec61 complex inhibited by ipomoeassin F
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8do1
Q-score: 0.511
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- Water (18 Da, Ligand)
- A human-yeast chimeric sec complex treated with ipomoeassin f (Complex from Homo sapiens)
- [(1~{s},3~{r},4~{s},5~{r},6~{r},8~{r},10~{s},23~{r},24~{r},25~{r},26~{r})-5-acetyloxy-6-methyl-4,26-bis(oxidanyl)-17,20-bis(oxidanylidene)-10-pentyl-24-[(~{e})-3-phenylprop-2-enoyl]oxy-2,7,9,21,27-pentaoxatricyclo[21.3.1.0^{3,8}]heptacosan-25-yl] (~{e})-2-methylbut-2-enoate (830 Da, Ligand)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human Sec61 complex inhibited by cyclotriazadisulfonamide (CADA)
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8do2
Q-score: 0.551
Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E
Nat Chem Biol (2023) 19 pp. 1063-1071 [ Pubmed: 37169959 DOI: doi:10.1038/s41589-023-01337-y ]
- 9-benzyl-1,5-bis(4-methylbenzene-1-sulfonyl)-3-methylidene-1,5,9-triazacyclododecane (581 Da, Ligand)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- A human-yeast chimeric sec complex treated with cyclotriazadisulfonamide (cada) (Complex from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)