SMTL ID : 8fs6.1

Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 4 (partially closed 9-1-1 and stably bound chamber DNA)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 24 residues within 4Å: Chain A: Y.67, F.70, K.71, P.72, Q.77, V.78, A.79, S.111, G.112, C.113, S.114, K.115, S.116, T.117, E.187, T.224, H.276, I.311, R.312, I.315 Chain B: R.128, P.153, R.157 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.77, A:A.79, A:G.112, A:C.113, A:S.114, A:S.114, A:K.115, A:K.115, A:S.116, A:T.117, A:T.117, A:T.224, A:T.224, A:R.312, A:R.312, B:R.128, B:R.157 Salt bridges: A:K.115, A:R.312, A:R.312 AGS.3: 25 residues within 4Å: Chain B: V.12, Y.15, R.16, P.17, D.22, I.23, V.24, P.51, G.52, I.53, G.54, K.55, T.56, T.57, N.145, L.166, R.174, M.202, R.203, I.206 Chain C: R.131, E.135, A.156, R.160 Ligands: MG.6 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:V.12, B:Y.15, B:V.24, B:G.52, B:I.53, B:I.53, B:G.54, B:K.55, B:K.55, B:T.56, B:T.56, B:T.57, B:N.145, B:R.203, C:R.131, C:R.160, C:R.160 Salt bridges: B:R.16, B:K.55, B:R.203, B:R.203 AGS.4: 25 residues within 4Å: Chain C: V.16, Y.19, R.20, P.21, E.26, V.27, Y.28, P.55, G.56, T.57, G.58, K.59, T.60, S.61, N.148, L.169, R.177, M.205, R.206, L.209 Chain D: R.154, E.158, P.179, R.183 Ligands: MG.5 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.19, C:R.20, C:Y.28, C:G.56, C:T.57, C:G.58, C:K.59, C:K.59, C:T.60, C:S.61, C:S.61, D:R.154, D:R.183 Salt bridges: C:R.20, C:K.59, C:R.206, C:R.206 AGS.7: 24 residues within 4Å: Chain D: V.28, Y.31, R.32, P.33, E.38, V.39, T.40, P.67, G.68, T.69, G.70, K.71, T.72, S.73, N.171, L.192, R.200, L.228, R.229 Chain E: R.155, E.159, P.180, R.184 Ligands: MG.8 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:V.28, D:T.40, D:G.68, D:T.69, D:T.69, D:T.69, D:G.70, D:K.71, D:T.72, D:T.72, D:S.73, D:S.73, D:R.229, D:R.229, E:R.155, E:R.184, E:R.184 Salt bridges: D:R.32, D:K.71, D:R.229, D:R.229

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.116, E.187 Ligands: AGS.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.116, A:E.187 MG.5: 5 residues within 4Å: Chain C: T.60, D.117, E.118 Chain D: R.183 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.60 MG.6: 4 residues within 4Å: Chain B: T.56 Chain C: E.135, R.160 Ligands: AGS.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:T.56, C:E.135 MG.8: 5 residues within 4Å: Chain D: T.72, D.140 Chain E: E.159, R.184 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.72

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

ADP.9: 19 residues within 4Å: Chain E: V.5, R.9, P.10, L.16, S.17, H.18, P.44, N.45, G.46, T.47, G.48, K.49, K.50, T.51, R.52, I.201, L.230, R.231, L.234 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:V.5, E:S.17, E:S.17, E:G.46, E:T.47, E:G.48, E:K.49, E:K.50, E:T.51, E:T.51, E:R.52 Salt bridges: E:R.9, E:K.49, E:R.231, E:R.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, F. et al., Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology. Biorxiv (2023)

Release Date

2023-06-14

Peptides

Checkpoint protein RAD24: A
Replication factor C subunit 4: B
Replication factor C subunit 3: C
Replication factor C subunit 2: D
Replication factor C subunit 5: E
DNA damage checkpoint control protein MEC3: F
DNA damage checkpoint control protein RAD17: G
DDC1 isoform 1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Checkpoint protein RAD24

Replication factor C subunit 4

Replication factor C subunit 3

Replication factor C subunit 2

Replication factor C subunit 5

DNA damage checkpoint control protein MEC3

DNA damage checkpoint control protein RAD17

DDC1 isoform 1

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