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: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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: https://doi.org/10.1038/s41586-018-0293-x
  • Primary Citation of Related Structures:  
    5ZR1

  • 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 DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element ...

    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: 

    Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA. biktye@ust.hk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 1A914Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC1, YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP54784
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2B620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC2, RRR1, SIR5, YBR060C, YBR0523
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 3C616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC3, OAF1, OIF1, YLL004W, L1365
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 4D529Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC4, YPR162C, P9325.5
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 5E479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC5, YNL261W, N0834
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Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP50874
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 6F435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC6, AAP1, YHR118C
UniProt
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Entity ID: 7
MoleculeChainsLengthOrganismImage
72bp-oring DNA, ACS305, T-richG72Saccharomyces cerevisiae
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Entity ID: 8
MoleculeChainsLengthOrganismImage
72bp-oring DNA, ACS305, A-richH72Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS
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I [auth A],
K [auth D],
M [auth E]		PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
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J [auth A],
L [auth D],
N [auth E]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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