SMTL ID : 8zpk.1

Cryo-EM structure of origin recognition complex (Orc6 with residues 1 to 270 deleted) with ARS1 DNA bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.21 Å

Oligo State

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

Ligands

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

AGS.1: 14 residues within 4Å: Chain B: V.8, A.9, R.11, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, Y.192, I.200, I.255 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.40, B:T.41, B:G.42, B:K.43, B:T.44, B:Y.45, B:Y.192, B:Y.192 Salt bridges: B:K.43 pi-Stacking: B:Y.45, B:Y.45 AGS.3: 19 residues within 4Å: Chain F: S.432, P.450, P.481, G.482, V.483, G.484, K.485, T.486, L.487, E.567, Y.627, I.635, R.639, R.704, L.707 Chain H: H.240, R.263, R.267 Ligands: MG.4 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain H Hydrogen bonds: F:G.482, F:V.483, F:G.484, F:K.485, F:T.486, F:L.487, F:E.567, F:Y.627, F:Y.627, F:R.639, F:R.704, H:H.240, H:R.267, H:R.267 Salt bridges: F:K.485, F:R.704, F:R.704 AGS.5: 12 residues within 4Å: Chain B: K.151 Chain H: P.103, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, D.113, K.338 Ligands: MG.6 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:Q.105, H:S.106, H:Y.107, H:K.108, H:T.109, H:Y.110, H:D.113, B:K.151 Salt bridges: H:K.108 pi-Stacking: H:Y.110

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.44, D.133 Ligands: AGS.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain F: T.486, E.567 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.486 MG.6: 2 residues within 4Å: Chain H: T.109 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lam, W.H. et al., DNA bending mediated by ORC is essential for replication licensing in budding yeast. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-04-16

Peptides

Origin recognition complex subunit 2: A
Origin recognition complex subunit 5: B
Origin recognition complex subunit 6: C
Origin recognition complex subunit 1: F
Origin recognition complex subunit 3: G
Origin recognition complex subunit 4: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
F

F
A

G
C

H
D

Origin recognition complex subunit 2

Origin recognition complex subunit 5

Origin recognition complex subunit 6

Origin recognition complex subunit 1

Origin recognition complex subunit 3

Origin recognition complex subunit 4

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