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 doc1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc26 (14 kDa, Protein from Saccharomyces cerevisiae)
- Hsl1 isoform 1 (169 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 1 (196 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc23 (73 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 4 (75 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Anaphase-promoting complex subunit cdc16 (96 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 cdc27 (85 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit swm1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 11 (18 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 2 (100 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 9 (30 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 5 (79 kDa, Protein from Saccharomyces cerevisiae)
- Cdh1 isoform 1 (62 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit mnd2 (42 kDa, Protein from Saccharomyces cerevisiae)
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 doc1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc26 (14 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 1 (196 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc23 (73 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 4 (75 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc16 (96 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase promoting complex/cyclosome (apc/c) (1 MDa, Complex from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc27 (85 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 11 (18 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit swm1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit mnd2 (42 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 9 (30 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 5 (79 kDa, Protein from Saccharomyces cerevisiae)
- Unphosphorylated apo apc/c complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Anaphase-promoting complex subunit 2 (100 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae apo phosphorylated APC/C
Resolution: 5.4 Å
EM Method: Single-particle
Fitted PDBs: 8a61
Q-score: 0.223
Barford D, Fernandez-Vazquez E, Zhang Z, Yang J
To Be Published
- Anaphase-promoting complex subunit doc1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc26 (14 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 1 (196 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc23 (73 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 4 (75 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc16 (96 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit cdc27 (85 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 11 (18 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit swm1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 2 (100 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 9 (30 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit 5 (79 kDa, Protein from Saccharomyces cerevisiae)
- Anaphase-promoting complex subunit mnd2 (42 kDa, Protein from Saccharomyces cerevisiae)
- Phosphorylated apo anaphase promoting complex/cyclosome (apc/c) (1 MDa, Complex from Saccharomyces cerevisiae)
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 [ DOI: doi:10.1038/s41586-022-04795-x Pubmed: 35676484 ]
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Water (18 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein 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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
Anaphase Promoting Complex delta APC7
Ferguson CJ, Urso O, Bodrug T, Gassaway BM, Watson ER, Prabu JR, Lara-Gonzalez P, Martinez-Chacin RC, Wu DY, Brigatti KW, Puffenberger EG, Taylor CM, Haas-Givler B, Jinks RN, Strauss KA, Desai A, Gabel HW, Gygi SP, Schulman BA, Brown NG, Bonni A
Mol Cell (2022) 82 pp. 90-105.e13 [ DOI: doi:10.1016/j.molcel.2021.11.031 Pubmed: 34942119 ]
- Anaphase promoting complex delta apc7 (1 MDa, Complex from Homo sapiens)
Anaphase Promoting Complex delta APC7 + UBE2C,substrate,UbV,CDH1
Ferguson CJ, Urso O, Bodrug T, Gassaway BM, Watson ER, Prabu JR, Lara-Gonzalez P, Martinez-Chacin RC, Wu DY, Brigatti KW, Puffenberger EG, Taylor CM, Haas-Givler B, Jinks RN, Strauss KA, Desai A, Gabel HW, Gygi SP, Schulman BA, Brown NG, Bonni A
Mol Cell (2022) 82 pp. 90-105.e13 [ DOI: doi:10.1016/j.molcel.2021.11.031 Pubmed: 34942119 ]
- Anaphase promoting complex delta apc7 (1 MDa, Complex from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-021-04145-3 Pubmed: 34700328 ]
- Protein timeless homolog (138 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm5 (82 kDa, Protein from Homo sapiens)
- Lagging strand dna (12 kDa, DNA from Homo sapiens)
- Human replisome engaged with cul2-lrr1 (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Leading strand dna (26 kDa, DNA from Homo sapiens)
- Dna polymerase epsilon subunit 2 (59 kDa, Protein from Homo sapiens)
- Dna polymerase epsilon catalytic subunit a (261 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Claspin (155 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Wd repeat and hmg-box dna-binding protein 1 (130 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm7 (81 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
- Dna replication licensing factor mcm3 (91 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm2 (102 kDa, Protein from Homo sapiens)
- Cell division control protein 45 homolog (66 kDa, Protein from Homo sapiens)
- Timeless-interacting protein (34 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf2 (21 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna replication licensing factor mcm4 (96 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein sld5 (30 kDa, Protein from Homo sapiens)
- Leucine-rich repeat protein 1 (46 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Dna replication complex gins protein psf1 (23 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (93 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf3 (24 kDa, Protein from Homo sapiens)
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 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA 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)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Supplementary proteins (Complex from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna damage-binding protein 1 (127 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 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Pig)
- 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)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Transcribing pol ii bound to trc factors, spt6 and paf. (Complex)
- Supplementary proteins (Complex from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2C (aka UBCH10)-substrate-Ubiquitin (variant)
Brown N, VanderLinden R, Watson E, Weissmann F, Ordureau A, Wu K-P, Yu S, Mercedi P, Harrison J, Davidson I, Coudevylle R, Lu Y, Dube P, Brunner M, Grace CRR, Miller D, Haselbach D, Jarvis M, Yamaguchi M, Yanishevski D, Petzold G, Sidhu S, Kuhlman B, Kirschner M, Harper JW, Peters J-M, Stark H, Schulman BA
Cell (2016) 165 pp. 1440-1453 [ DOI: doi:10.1016/j.cell.2016.05.037 Pubmed: 27259151 ]