Human OCCM DNA licensing intermediate
Resolution: 6.68 Å
EM Method: Single-particle
Fitted PDBs: 8rwv
Q-score: 0.186
Wells JN, Edwardes LV, Leber V, Allyjaun S, Peach M, Tomkins J, Kefala-Stavridi A, Faull SV, Aramayo R, Pestana CM, Ranjha L, Speck C
Nat Commun (2025) 16 pp. 478-478 [ Pubmed: 39779677 DOI: doi:10.1038/s41467-024-55772-z ]
- Dna replication factor cdt1 (46 kDa, Protein from Homo sapiens)
- Isoform 2 of dna replication licensing factor mcm3 (96 kDa, Protein from Homo sapiens)
- Origin recognition complex subunit 1 (108 kDa, Protein from Homo sapiens)
- Origin recognition complex subunit 5 (50 kDa, Protein from Homo sapiens)
- Origin recognition complex subunit 4 (50 kDa, Protein from Homo sapiens)
- Dna (11 kDa, DNA from Homo sapiens)
- Dna replication licensing factor mcm2 (106 kDa, Protein from Homo sapiens)
- Origin recognition complex subunit 2 (66 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm7 (81 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm4 (99 kDa, Protein from Homo sapiens)
- Hoccm (1 MDa, Complex from Homo sapiens)
- Isoform 2 of origin recognition complex subunit 3 (82 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm6 (93 kDa, Protein from Homo sapiens)
- Cell division control protein 6 homolog (62 kDa, Protein from Homo sapiens)
- Dna (12 kDa, DNA from Homo sapiens)
Structure of yeast replisome associated with FACT and histone hexamer, Composite map
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8xgc
Q-score: 0.407
Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, Zhou K, Liu Y, Li XD, Tye BK, Li Q, Gao N, Zhai Y
Nature (2024) 627 pp. 890-897 [ DOI: doi:10.1038/s41586-024-07152-2 Pubmed: 38448592 ]
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b.2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna (51-mer) (15 kDa, DNA from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of replication checkpoint protein 1 (124 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Endogenous replisomes (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (29 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit spt16 (118 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit pob3 (63 kDa, Protein from Saccharomyces cerevisiae)
- Dna (39-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state iv (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8kg6
Q-score: 0.437
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 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state i (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.23 Å
EM Method: Single-particle
Fitted PDBs: 8kg8
Q-score: 0.246
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 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state ii (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 8kg9
Q-score: 0.19
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 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (70-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state ii (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8w7m
Q-score: 0.267
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 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Replisome complex in state v (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA)
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 7w1y
Q-score: 0.595
Li J, Dong J, Wang W, Yu D, Fan X, Hui YC, Lee CSK, Lam WH, Alary N, Yang Y, Zhang Y, Zhao Q, Chen CL, Tye BK, Dang S, Zhai Y
Cell (2023) 186 pp. 98-111.e21 [ Pubmed: 36608662 DOI: doi:10.1016/j.cell.2022.12.008 ]
- Dna replication licensing factor mcm5 (82 kDa, Protein from Homo sapiens)
- Dna (49-mer) (14 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Isoform 2 of dna replication licensing factor mcm3 (96 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm6 (93 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication licensing factor mcm4 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Human mini-chromosome maintenance complex (1 MDa, Complex from Homo sapiens)
- Dna replication licensing factor mcm7 (81 kDa, Protein from Homo sapiens)
- Dna (49-mer) (15 kDa, DNA from Homo sapiens)
- Dna replication licensing factor mcm2 (102 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Dna replication licensing factor mcm 2/3/4/5/6/7 (Complex from Homo sapiens)
Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III (composite map)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7pt6
Q-score: 0.525
Saleh A, Noguchi Y, Aramayo R, Ivanova ME, Stevens KM, Montoya A, Sunidhi S, Carranza NL, Skwark MJ, Speck C
Nat Commun (2022) 13 pp. 2915-2915 [ Pubmed: 35614055 DOI: doi:10.1038/s41467-022-30576-1 ]
- Undefined mcm4 flexible n-terminal tail (358 Da, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Cell division control protein 7 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ddk kinase regulatory subunit dbf4 (80 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mcm2-7 double hexamer bound to two copies of cdc7-dbf4 (1 MDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I (composite map)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7pt7
Q-score: 0.445
Saleh A, Noguchi Y, Aramayo R, Ivanova ME, Stevens KM, Montoya A, Sunidhi S, Carranza NL, Skwark MJ, Speck C
Nat Commun (2022) 13 pp. 2915-2915 [ Pubmed: 35614055 DOI: doi:10.1038/s41467-022-30576-1 ]
- Undefined mcm4 flexible n-terminal tail (358 Da, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Cell division control protein 7 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mcm2-7 double hexamer bound to one copy of cdc7-dbf4 (1 MDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ddk kinase regulatory subunit dbf4 (80 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))