SMTL ID : 6xtx.1

CryoEM structure of human CMG bound to ATPgammaS and DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.329, C.332, C.352, C.355 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.329, A:C.332, A:C.352, A:C.355 ZN.4: 5 residues within 4Å: Chain C: C.326, C.329, C.348, C.351, S.356 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.326, C:C.329, C:C.348, C:C.351 ZN.8: 5 residues within 4Å: Chain D: C.172, S.174, C.175, C.197, C.207 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197, D:C.207 ZN.9: 5 residues within 4Å: Chain E: C.158, D.160, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180, E:C.185 ZN.11: 4 residues within 4Å: Chain F: C.184, C.187, C.206, C.211 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.184, F:C.187, F:C.206, F:C.211

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 11 residues within 4Å: Chain A: P.525, G.526, T.527, A.528, K.529, S.530, Q.531, L.675 Chain E: V.618, R.619, E.622 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:G.526, A:T.527, A:A.528, A:K.529, A:S.530, A:S.530, A:Q.531 Salt bridges: A:K.529, E:R.619, E:R.619 ADP.3: 14 residues within 4Å: Chain B: S.351, I.352, H.353, P.392, S.393, V.394, A.395, K.396, S.397 Chain D: R.371, E.463, V.610, R.611, E.614 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.353, B:H.353, B:S.393, B:V.394, B:A.395, B:K.396, B:S.397, B:S.397, B:Q.398, D:R.371, D:R.371 Salt bridges: B:K.396

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.5: 20 residues within 4Å: Chain C: S.489, I.490, Y.491, P.532, G.533, S.535, K.536, S.537, Q.538, N.638, L.682, L.686 Chain F: M.369, I.371, Q.464, A.510, R.514, R.604, L.607 Ligands: MG.6 17 PLIP interactions: 4 interactions with chain F, 13 interactions with chain C Hydrogen bonds: F:Q.464, F:R.514, C:Y.491, C:G.533, C:S.535, C:K.536, C:K.536, C:S.537, C:S.537, C:Q.538, C:N.638, C:N.638, C:Y.678, C:Y.678 Salt bridges: F:R.604, F:R.604, C:K.536 AGS.7: 14 residues within 4Å: Chain C: R.517, R.663, R.752, E.755 Chain E: H.359, S.399, T.400, A.401, K.402, S.403, N.504, I.548, I.552 Ligands: MG.10 15 PLIP interactions: 10 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:H.359, E:H.359, E:S.399, E:T.400, E:T.400, E:A.401, E:K.402, E:S.403, E:N.504, C:R.517, C:R.517, C:R.663, C:E.755 Salt bridges: E:K.402, C:R.752 AGS.12: 19 residues within 4Å: Chain B: E.472, Q.473, R.523, A.660, R.661, E.664 Chain F: E.343, I.344, Y.345, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, N.489, L.533 Ligands: MG.13 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain F Hydrogen bonds: B:Q.473, B:R.523, B:R.523, F:Y.345, F:Y.345, F:G.384, F:V.385, F:A.386, F:K.387, F:K.387, F:S.388, F:Q.389, F:N.489, F:N.489 Salt bridges: B:R.661, B:R.661, F:K.387

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain C: S.537, D.594 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.537 MG.10: 2 residues within 4Å: Chain E: S.403 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.403 MG.13: 3 residues within 4Å: Chain B: Q.473 Chain F: S.388 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rzechorzek, N.J. et al., CryoEM structures of human CMG-ATP gamma S-DNA and CMG-AND-1 complexes. Nucleic Acids Res. (2020)

Release Date

2020-05-27

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
DNA replication licensing factor MCM5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
DNA replication complex GINS protein PSF1: G
DNA replication complex GINS protein PSF2: H
DNA replication complex GINS protein PSF3: I
DNA replication complex GINS protein SLD5: J
Cell division control protein 45 homolog: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
A

H
B

I
C

J
D

K
E

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45 homolog

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