4XGC

Crystal structure of the eukaryotic origin recognition complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    4XGC

  • 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 Drosophila ORC at 3 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2A [auth B]354Drosophila melanogasterMutation(s): 0 
Gene Names: Orc2CG3041
UniProt
Find proteins for Q24168 (Drosophila melanogaster)
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Go to UniProtKB:  Q24168
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 3B [auth C]676Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q7K2L1 (Drosophila melanogaster)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 5C [auth E]460Drosophila melanogasterMutation(s): 0 
Gene Names: Orc5CG7833
UniProt
Find proteins for Q24169 (Drosophila melanogaster)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 1D [auth A]393Drosophila melanogasterMutation(s): 0 
Gene Names: Orc1CG10667
UniProt
Find proteins for O16810 (Drosophila melanogaster)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2E [auth G]41Drosophila melanogasterMutation(s): 0 
Gene Names: Orc2CG3041
Protein Feature View
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 6F72Drosophila melanogasterMutation(s): 0 
Gene Names: Orc6CG1584
UniProt
Find proteins for Q9Y1B2 (Drosophila melanogaster)
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 4G [auth D]459Drosophila melanogasterMutation(s): 0 
Gene Names: orc4CG2917Dmel_CG2917Orc4Dmel\CG2917DmORC4dmOrc4ORCORC4rDmORC
EC: 3.6.1.15
UniProt
Find proteins for Q9W102 (Drosophila melanogaster)
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
H [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth E]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.545α = 90
b = 258.983β = 90
c = 257.001γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata scaling
SHELXphasing
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071747
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA R37-30490

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Data collection
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence