5MLW

Crystal structure of human PCNA in complex with ZRANB3 APIM motif peptide

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-12-07 Released: 2017-06-28 
  • Deposition Author(s): Ariza, A.
  • Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report



Literature

Structural insights into the function of ZRANB3 in replication stress response.

Sebesta, M.Cooper, C.D.O.Ariza, A.Carnie, C.J.Ahel, D.

(2017) Nat Commun 8: 15847-15847

  • DOI: 10.1038/ncomms15847
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Strategies to resolve replication blocks are critical for the maintenance of genome stability. Among the factors implicated in the replication stress response is the ATP-dependent endonuclease ZRANB3. Here, we present the structure of the ZRANB3 HNH ...

    Strategies to resolve replication blocks are critical for the maintenance of genome stability. Among the factors implicated in the replication stress response is the ATP-dependent endonuclease ZRANB3. Here, we present the structure of the ZRANB3 HNH (His-Asn-His) endonuclease domain and provide a detailed analysis of its activity. We further define PCNA as a key regulator of ZRANB3 function, which recruits ZRANB3 to stalled replication forks and stimulates its endonuclease activity. Finally, we present the co-crystal structures of PCNA with two specific motifs in ZRANB3: the PIP box and the APIM motif. Our data provide important structural insights into the PCNA-APIM interaction, and reveal unexpected similarities between the PIP box and the APIM motif. We propose that PCNA and ATP-dependency serve as a multi-layered regulatory mechanism that modulates ZRANB3 activity at replication forks. Importantly, our findings allow us to interpret the functional significance of cancer associated ZRANB3 mutations.


    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C, E
261Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS  P12004
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
APIM motif peptide
B, D, F
11Homo sapiensMutation(s): 0 
Gene Names: ZRANB3
EC: 3.6.4 (UniProt), 3.1 (UniProt)
Find proteins for Q5FWF4 (Homo sapiens)
Go to UniProtKB:  Q5FWF4
NIH Common Fund Data Resources
PHAROS  Q5FWF4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, C, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.631α = 90
b = 84.631β = 90
c = 201.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-07 
  • Released Date: 2017-06-28 
  • Deposition Author(s): Ariza, A.

Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom16304

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release