6P3W

Crystal structure of the Cyclin A-CDK2-ORC1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Literature

Structural basis for the ORC1-Cyclin A association.

Wang, B.Song, J.

(2019) Protein Sci 28: 1727-1733

  • DOI: 10.1002/pro.3689
  • Primary Citation of Related Structures:  
    6P3W

  • PubMed Abstract: 
  • Progression of cell cycle is regulated by sequential expression of cyclins, which associate with distinct cyclin kinases to drive the transition between different cell cycle phases. The complex of Cyclin A with cyclin-dependent kinase 2 (CDK2) controls the DNA replication activity through phosphorylation of a set of chromatin factors, which critically influences the S phase transition ...

    Progression of cell cycle is regulated by sequential expression of cyclins, which associate with distinct cyclin kinases to drive the transition between different cell cycle phases. The complex of Cyclin A with cyclin-dependent kinase 2 (CDK2) controls the DNA replication activity through phosphorylation of a set of chromatin factors, which critically influences the S phase transition. It has been shown that the direct interaction between the Cyclin A-CDK2 complex and origin recognition complex subunit 1 (ORC1) mediates the localization of ORC1 to centrosomes, where ORC1 inhibits cyclin E-mediated centrosome reduplication. However, the molecular basis underlying the specific recognition between ORC1 and cyclins remains elusive. Here we report the crystal structure of Cyclin A-CDK2 complex bound to a peptide derived from ORC1 at 2.54 å resolution. The structure revealed that the ORC1 peptide interacts with a hydrophobic groove, termed cyclin binding groove (CBG), of Cyclin A via a KXL motif. Distinct from other identified CBG-binding sequences, an arginine residue flanking the KXL motif of ORC1 inserts into a neighboring acidic pocket, contributing to the strong ORC1-Cyclin A association. Furthermore, structural and sequence analysis of cyclins reveals divergence on the ORC1-binding sites, which may underpin their differential ORC1-binding activities. This study provides a structural basis of the specific ORC1-cyclins recognition, with implication in development of novel inhibitors against the cyclin/CDK complexes.


    Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, California.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2A, D [auth C]298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
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Find proteins for P24941 (Homo sapiens)
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PHAROS:  P24941
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-A2B, E [auth D]257Homo sapiensMutation(s): 0 
Gene Names: CCNA2CCN1CCNA
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Find proteins for P20248 (Homo sapiens)
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PHAROS:  P20248
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ORC1 PeptideC [auth E], F7Homo sapiensMutation(s): 0 
Gene Names: ORC1ORC1LPARC1
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Find proteins for Q13415 (Homo sapiens)
Explore Q13415 
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PHAROS:  Q13415
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.396α = 90
b = 186.396β = 90
c = 214.707γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-05-24 
  • Released Date: 2019-07-31 
  • Deposition Author(s): Wang, B., Song, J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references