4XGC

Crystal structure of the eukaryotic origin recognition complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the eukaryotic origin recognition complex.

Bleichert, F.Botchan, M.R.Berger, J.M.

(2015) Nature 519: 321-326

  • DOI: 10.1038/nature14239

  • PubMed Abstract: 
  • Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset. Here we describe the crystal structure of ...

    Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset. Here we describe the crystal structure of Drosophila ORC at 3.5 Å resolution, showing that the 270 kilodalton initiator core complex comprises a two-layered notched ring in which a collar of winged-helix domains from the Orc1-5 subunits sits atop a layer of AAA+ (ATPases associated with a variety of cellular activities) folds. Although canonical inter-AAA+ domain interactions exist between four of the six ORC subunits, unanticipated features are also evident. These include highly interdigitated domain-swapping interactions between the winged-helix folds and AAA+ modules of neighbouring protomers, and a quasi-spiral arrangement of DNA binding elements that circumnavigate an approximately 20 Å wide channel in the centre of the complex. Comparative analyses indicate that ORC encircles DNA, using its winged-helix domain face to engage the mini-chromosome maintenance 2-7 (MCM2-7) complex during replicative helicase loading; however, an observed out-of-plane rotation of more than 90° for the Orc1 AAA+ domain disrupts interactions with catalytic amino acids in Orc4, narrowing and sealing off entry into the central channel. Prima facie, our data indicate that Drosophila ORC can switch between active and autoinhibited conformations, suggesting a novel means for cell cycle and/or developmental control of ORC functions.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 2
B
354Drosophila melanogasterMutation(s): 0 
Gene Names: Orc2
Find proteins for Q24168 (Drosophila melanogaster)
Go to UniProtKB:  Q24168
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 3
C
676Drosophila melanogasterMutation(s): 0 
Gene Names: Orc3 (CG34315-RB, Dmel\CG4088, DmORC3, DmOrc3, l(2)49Fd, l(2)vr6, LAT, Lat, lat, lat-RA, latheo, ORC, ORC3, orc3, vr-6, vr6)
Find proteins for Q7K2L1 (Drosophila melanogaster)
Go to UniProtKB:  Q7K2L1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 5
E
460Drosophila melanogasterMutation(s): 0 
Gene Names: Orc5
Find proteins for Q24169 (Drosophila melanogaster)
Go to UniProtKB:  Q24169
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 1
A
393Drosophila melanogasterMutation(s): 0 
Gene Names: Orc1
Find proteins for O16810 (Drosophila melanogaster)
Go to UniProtKB:  O16810
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 2
G
41N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 6
F
72Drosophila melanogasterMutation(s): 0 
Gene Names: Orc6
Find proteins for Q9Y1B2 (Drosophila melanogaster)
Go to UniProtKB:  Q9Y1B2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Origin recognition complex subunit 4
D
459Drosophila melanogasterMutation(s): 0 
Gene Names: Orc4 (Dmel\CG2917, DmORC4, dmOrc4, ORC, ORC4, orc4, rDmORC)
Find proteins for Q9W102 (Drosophila melanogaster)
Go to UniProtKB:  Q9W102
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 145.545α = 90.00
b = 258.983β = 90.00
c = 257.001γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071747
National Institutes of Health/National Cancer InstituteUnited StatesCA R37-30490

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Data collection
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description