5HH7

crystal structure of Arabidopsis ORC1b BAH-PHD cassette in complex with unmodified H3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette

Li, S.Yang, Z.Du, X.Liu, R.Wilkinson, A.W.Gozani, O.Jacobsen, S.E.Patel, D.J.Du, J.

(2016) Structure 24: 486-494

  • DOI: https://doi.org/10.1016/j.str.2016.01.004
  • Primary Citation of Related Structures:  
    5HH7

  • PubMed Abstract: 

    DNA replication initiation relies on the formation of the origin recognition complex (ORC). The plant ORC subunit 1 (ORC1) protein possesses a conserved N-terminal BAH domain with an embedded plant-specific PHD finger, whose function may be potentially regulated by an epigenetic mechanism. Here, we report structural and biochemical studies on the Arabidopsis thaliana ORC1b BAH-PHD cassette which specifically recognizes the unmodified H3 tail. The crystal structure of ORC1b BAH-PHD cassette in complex with an H3(1-15) peptide reveals a strict requirement for the unmodified state of R2, T3, and K4 on the H3 tail and a novel multivalent BAH and PHD readout mode for H3 peptide recognition. Such recognition may contribute to epigenetic regulation of the initiation of DNA replication.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Origin of replication complex subunit 1B233Arabidopsis thalianaMutation(s): 0 
Gene Names: ORC1BUNE13At4g12620T1P17.210
UniProt
Find proteins for Q9SU24 (Arabidopsis thaliana)
Explore Q9SU24 
Go to UniProtKB:  Q9SU24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SU24
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3 1-15 peptideB [auth P]15Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59226 (Arabidopsis thaliana)
Explore P59226 
Go to UniProtKB:  P59226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59226
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.408α = 90
b = 64.408β = 90
c = 79.633γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2016-03-09 
  • Deposition Author(s): Li, S., Du, J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations