5ZR1

Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the origin recognition complex bound to DNA replication origin.

Li, N.Lam, W.H.Zhai, Y.Cheng, J.Cheng, E.Zhao, Y.Gao, N.Tye, B.K.

(2018) Nature 559: 217-222

  • DOI: 10.1038/s41586-018-0293-x

  • PubMed Abstract: 
  • The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin ...

    The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element. The ORC encircles DNA through extensive interactions with both phosphate backbone and bases, and bends DNA at the ACS and B1 sites. Specific recognition of thymine residues in the ACS is carried out by a conserved basic amino acid motif of Orc1 in the minor groove, and by a species-specific helical insertion motif of Orc4 in the major groove. Moreover, similar insertions into major and minor grooves are also embedded in the B1 site by basic patch motifs from Orc2 and Orc5, respectively, to contact bases and to bend DNA. This work pinpoints a conserved role of ORC in modulating DNA structure to facilitate origin selection and helicase loading in eukaryotes.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 1
A
914Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC1
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC1
Go to UniProtKB:  P54784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 2
B
620Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC2 (RRR1, SIR5)
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC2
Go to UniProtKB:  P32833
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 3
C
616Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC3 (OAF1, OIF1)
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC3
Go to UniProtKB:  P54790
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 4
D
529Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC4
Find proteins for P54791 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC4
Go to UniProtKB:  P54791
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 5
E
479Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC5
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC5
Go to UniProtKB:  P50874
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 6
F
435Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ORC6 (AAP1)
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ORC6
Go to UniProtKB:  P38826
Entity ID: 7
MoleculeChainsLengthOrganism
72bp-oring DNA, ACS305, T-richG72Saccharomyces cerevisiae
Entity ID: 8
MoleculeChainsLengthOrganism
72bp-oring DNA, ACS305, A-richH72Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
A, D, E
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references