Resolution: 7.39 Å
EM Method: Single-particle
Fitted PDBs: 8w7s
Q-score: 0.212
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
Nat Commun (2023) 14 pp. 5849-5849 [ DOI: doi:10.1038/s41467-023-41506-0 Pubmed: 37730685 ]
- Replisome complex in state iv (1 MDa, Complex from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
Mediator-PIC Early (Tail A + Upstream DNA Activator)
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 7uik
Q-score: 0.091
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574- [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
- Mediator of rna polymerase ii transcription subunit 5 (128 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Med-picearly (taila+activator & dna class 1) (Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 2 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 14 (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 16 (111 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 15 (120 kDa, Protein from Saccharomyces cerevisiae S288C)
- Regulatory protein gal4 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 3 (43 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
Resolution: 6.54 Å
EM Method: Single-particle
Fitted PDBs: 7e93
Q-score: 0.153
Mi C, Zhang L, Huang G, Shao G, Yang F, You X, Dong MQ, Sun S, Sui SF
Sci Adv (2022) 8 pp. eabi5603-eabi5603 [ Pubmed: 35080977 DOI: doi:10.1126/sciadv.abi5603 ]
- Trafficking protein particle complex ii-specific subunit 130 (128 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex subunit 33 (30 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trapp-associated protein tca17 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex ii-specific subunit 65 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Intact trappii (state iii). (Complex from Saccharomyces cerevisiae)
- Trafficking protein particle complex ii-specific subunit 120 (147 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex subunit bet3 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex subunit 23 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex subunit 31 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex subunit bet5 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Trafficking protein particle complex subunit 20 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
CryoEM Structures of Reconstituted V-ATPase, state3
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7fdc
Q-score: 0.069
Khan MM, Lee S, Oot RA, Couoh-Cardel S, Kim H, Wilkens S, Roh SH
EMBO J (2021) [ ]
- Chimeric subunit h (Complex from Saccharomyces cerevisiae S288c)
- V-type proton atpase subunits (Complex)
- V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit g (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast vacuolar atpase c subunit (Complex from Saccharomyces cerevisiae S288c)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast vacuolar atpase f subunit (9 kDa, Protein from Saccharomyces cerevisiae S288C)
- Fusion of yeast v-type proton atpase subunit h(nt) and human v-type proton atpase subunit h(ct) (53 kDa, Protein from Homo sapiens)
- Yeast vacuolar atpase a subunit (67 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast vacuolar atpase a subunit (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- V-type proton atpase subunit c (44 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast vacuolar atpase in rotary state 3 (1 MDa, Complex from Saccharomyces cerevisiae S288c)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 7oa6
Q-score: 0.133
Muhlhofer M, Peters C, Kriehuber T, Kreuzeder M, Kazman P, Rodina N, Reif B, Haslbeck M, Weinkauf S, Buchner J
Nat Commun (2021) 12 pp. 6697-6697 [ DOI: doi:10.1038/s41467-021-27036-7 Pubmed: 34795272 ]
Structure of a yeast ABCE1-bound 48S initiation complex
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 6zu9
Q-score: 0.22
Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R
EMBO J (2021) 40 pp. e105179-e105179 [ Pubmed: 33289941 DOI: doi:10.15252/embj.2020105179 ]
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 1a (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 3 subunit a (110 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 5 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Trna (24 kDa, RNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Rps5p (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 3 subunit c (93 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 3 subunit g (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- 40s ribosomal protein s26-a (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 3 subunit i (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s28-b (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mrna (2 kDa, RNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Eukaryotic translation initiation factor 3 subunit b (88 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Abce1-bound 48s initiation complex (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Translation initiation factor rli1 (68 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s29-a (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s15 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Head segment of the S.cerevisiae condensin holocomplex in presence of ATP
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 6yvd
Q-score: 0.16
Lee BG, Merkel F, Allegretti M, Hassler M, Cawood C, Lecomte L, O'Reilly FJ, Sinn LR, Gutierrez-Escribano P, Kschonsak M, Bravo S, Nakane T, Rappsilber J, Aragon L, Beck M, Lowe J, Haering CH
Nat Struct Mol Biol (2020) 27 pp. 743-751 [ DOI: doi:10.1038/s41594-020-0457-x Pubmed: 32661420 ]
- Condensin (650 kDa, Complex from Saccharomyces cerevisiae S288C)
- Condensin complex subunit 2 (92 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Structural maintenance of chromosomes protein 2 (134 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Condensin complex subunit 3 (117 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Structural maintenance of chromosomes protein 4 (168 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
The ClassA RSC-Nucleosome Complex
Resolution: 7.13 Å
EM Method: Single-particle
Fitted PDBs: 6kw3
Q-score: 0.086
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
The ClassB RSC-Nucleosome Complex
Resolution: 7.55 Å
EM Method: Single-particle
Fitted PDBs: 6kw4
Q-score: 0.099
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Saccharomyces cerevisiae S288C)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
The structure of a Ty3 retrotransposon icosahedral capsid
Resolution: 7.5 Å
EM Method: Single-particle
Fitted PDBs: 6r24
Q-score: 0.297
Dodonova SO, Prinz S, Bilanchone V, Sandmeyer S, Briggs JAG
PNAS (2019) 116 pp. 10048-10057 [ Pubmed: 31036670 DOI: doi:10.1073/pnas.1900931116 ]