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S. cerevisiae APC/C-Cdh1 complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8a3t
Q-score: 0.336
Barford D, Vazquez-Fernandez E, Zhang Z, Yang J
To Be Published
- Anaphase-promoting complex subunit 4 (75 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 9 (30 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 11 (18 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc27 (85 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase promoting complex/cyclosome (apc/c) in complex with cdh1 and hsl1 (1 MDa, Complex from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 5 (79 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 1 (196 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc26 (14 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit swm1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit doc1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc23 (73 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 2 (100 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit mnd2 (42 kDa, Protein from Saccharomyces cerevisiae)
- Cdh1 isoform 1 (62 kDa, Protein from Saccharomyces cerevisiae)
- Hsl1 isoform 1 (169 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc16 (96 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
S. cerevisiae apo unphosphorylated APC/C
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 8a5y
Q-score: 0.192
Barford D, Fernandez-Vazquez E, Zhang Z, Yang J
To Be Published
- Anaphase-promoting complex subunit 4 (75 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 9 (30 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 11 (18 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc27 (85 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 5 (79 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 1 (196 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc26 (14 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit swm1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Unphosphorylated apo apc/c complex (Complex from Saccharomyces cerevisiae)
- Anaphase promoting complex/cyclosome (apc/c) (1 MDa, Complex from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit doc1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc23 (73 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 2 (100 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit mnd2 (42 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc16 (96 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 7pnt
Q-score: 0.516
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- Water (18 Da, Ligand)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
H. sapiens replisome-CUL2/LRR1 complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7plo
Q-score: 0.415
Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD
Nature (2021) 600 pp. 743-747 [ Pubmed: 34700328 DOI: doi:10.1038/s41586-021-04145-3 ]
- Timeless-interacting protein (34 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm3 (91 kDa, Protein from Homo sapiens)
- Cell division control protein 45 homolog (66 kDa, Protein from Homo sapiens)
- Lagging strand dna (12 kDa, DNA from Homo sapiens)
- Dna replication licensing factor mcm5 (82 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf1 (23 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Claspin (155 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf2 (21 kDa, Protein from Homo sapiens)
- Dna polymerase epsilon catalytic subunit a (261 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm6 (93 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm2 (102 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein sld5 (30 kDa, Protein from Homo sapiens)
- Wd repeat and hmg-box dna-binding protein 1 (130 kDa, Protein from Homo sapiens)
- Leading strand dna (26 kDa, DNA from Homo sapiens)
- Dna replication licensing factor mcm4 (96 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf3 (24 kDa, Protein from Homo sapiens)
- Protein timeless homolog (138 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Leucine-rich repeat protein 1 (46 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Dna polymerase epsilon subunit 2 (59 kDa, Protein from Homo sapiens)
- Human replisome engaged with cul2-lrr1 (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm7 (81 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opc
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Supplementary proteins (Complex from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opd
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Supplementary proteins (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to trc factors, spt6 and paf. (Complex)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Pig)