SMTL ID : 8zp4.1

Cryo-EM structure of origin recognition complex (Orc1 to 5) with ARS1 DNA bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.33 Å

Oligo State

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

Ligands

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

AGS.1: 21 residues within 4Å: Chain A: S.432, L.449, P.450, R.452, P.481, G.482, V.483, G.484, K.485, T.486, L.487, E.567, Y.627, I.635, R.639, A.703, R.704 Chain D: H.240, R.263, R.267 Ligands: MG.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.432, A:G.482, A:V.483, A:G.484, A:K.485, A:T.486, A:T.486, A:L.487, A:Y.627, A:R.639, A:R.704, D:H.240, D:R.267, D:R.267 Salt bridges: A:K.485, A:R.704, A:R.704 AGS.3: 15 residues within 4Å: Chain D: Y.61, G.62, K.69, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, E.218, K.338 Chain G: K.151, K.158 Ligands: MG.4 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:K.69, D:Q.105, D:S.106, D:Y.107, D:Y.107, D:K.108, D:T.109, D:Y.110, D:K.338, G:K.151, G:K.151 Salt bridges: D:K.108 AGS.5: 16 residues within 4Å: Chain G: A.9, F.10, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, Y.192, I.200, S.204, I.255, F.256 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:A.9, G:F.10, G:G.40, G:T.41, G:G.42, G:K.43, G:K.43, G:T.44, G:T.44, G:Y.45, G:Y.192, G:Y.192, G:S.204 Salt bridges: G:K.43 pi-Stacking: G:Y.45

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.486 Chain D: R.267 Ligands: AGS.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain D: T.109, D.217 Chain G: K.151, E.154 Ligands: AGS.3 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain G Metal complexes: D:T.109, G:E.154 MG.6: 3 residues within 4Å: Chain G: T.44, D.133 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.44

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 1: A
Origin recognition complex subunit 2: B
Origin recognition complex subunit 3: C
Origin recognition complex subunit 4: D
Origin recognition complex subunit 5: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
E

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 4

Origin recognition complex subunit 5

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