SMTL ID : 5v8f.1

Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 20 residues within 4Å: Chain A: S.504, I.505, Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, V.699 Chain E: E.657, Q.658, P.704, R.708, V.797, R.798, E.801 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:A.548, A:K.549, A:S.550, A:Q.551, A:E.608, A:E.608, A:N.651, E:E.657, E:R.708 Salt bridges: A:K.549, A:K.549, E:R.708, E:R.798, E:R.798 AGS.2: 17 residues within 4Å: Chain C: S.529, I.530, Y.531, L.533, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720 Chain F: M.448, I.450, R.593, P.686, R.687 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:Y.531, C:S.571, C:T.572, C:S.573, C:S.573, C:K.574, C:K.574, C:S.575, C:Q.576, C:Q.576, C:Q.576, F:R.593 Salt bridges: F:R.593, F:R.687, F:R.687 AGS.3: 14 residues within 4Å: Chain C: E.650, Q.651, R.701, T.795, R.796 Chain E: F.538, S.578, T.579, S.580, K.581, S.582, E.640, N.683, I.731 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:F.538, E:S.578, E:T.579, E:S.580, E:S.580, E:K.581, E:S.582, E:E.640, E:E.640, E:N.683, C:T.795 Salt bridges: C:R.701, C:R.796, C:R.796 AGS.4: 18 residues within 4Å: Chain B: E.491, R.542, R.700, E.703 Chain F: I.422, Y.423, G.460, D.461, P.462, G.463, A.465, K.466, S.467, Q.468, D.524, N.568, L.612, V.616 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:Y.423, F:Y.423, F:A.465, F:K.466, F:S.467, F:Q.468, F:Q.468, F:D.524, B:R.542 Salt bridges: B:R.542, B:R.542 AGS.5: 16 residues within 4Å: Chain H: G.108, P.109, P.110, G.111, T.112, G.113, K.114, T.115, A.116, Y.291, Q.295, M.296, I.299 Chain I: K.612, S.615, R.616 15 PLIP interactions: 12 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:G.108, H:P.109, H:G.111, H:T.112, H:G.113, H:K.114, H:T.115, H:T.115, H:T.115, H:A.116, H:N.263, H:Q.295, I:S.615 Salt bridges: I:R.616, I:R.616 AGS.6: 18 residues within 4Å: Chain I: S.432, L.449, P.481, G.482, V.483, G.484, K.485, T.486, L.487, D.566, E.567, Y.627, I.635, R.639, A.703, R.704, L.707 Chain M: R.267 21 PLIP interactions: 18 interactions with chain I, 3 interactions with chain M Hydrogen bonds: I:S.432, I:G.482, I:V.483, I:G.484, I:K.485, I:T.486, I:T.486, I:L.487, I:D.566, I:E.567, I:E.567, I:R.639, I:R.704, I:R.704, M:R.267, M:R.267 Salt bridges: I:K.485, I:K.485, I:R.704, I:R.704, M:R.267 AGS.7: 12 residues within 4Å: Chain L: V.8, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, Y.192, I.200, F.256 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:G.40, L:T.41, L:G.42, L:K.43, L:T.44, L:T.44, L:Y.45 Salt bridges: L:K.43 pi-Stacking: L:Y.45 AGS.8: 13 residues within 4Å: Chain L: E.154, K.158 Chain M: Y.61, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, E.218, P.335, K.338 13 PLIP interactions: 2 interactions with chain L, 11 interactions with chain M Hydrogen bonds: L:E.154, L:K.158, M:Q.105, M:Q.105, M:S.106, M:Y.107, M:K.108, M:T.109, M:T.109, M:T.109, M:Y.110, M:E.218 Salt bridges: M:K.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, Z. et al., Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-05-10

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
Minichromosome maintenance protein 5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
Cell division cycle protein CDT1: G
Cell division control protein 6: H
Origin recognition complex subunit 1: I
Origin recognition complex subunit 2: J
Origin recognition complex subunit 3: K
Origin recognition complex subunit 5: L
Origin recognition complex subunit 4: M
Origin recognition complex subunit 6: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
8

H
9

I
A

J
B

K
C

L
E

M
D

N
F

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

Minichromosome maintenance protein 5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

Cell division cycle protein CDT1

Cell division control protein 6

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 5

Origin recognition complex subunit 4

Origin recognition complex subunit 6

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