5N8A | pdb_00005n8a

Structure of RPA70N in complex with PrimPol (fragment 480-560)

• PDB DOI: https://doi.org/10.2210/pdb5N8A/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2017-02-23 Released: 2017-06-07 
• Deposition Author(s): Brissett, N.C., Doherty, A.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for PrimPol recruitment to replication forks by RPA.

Guilliam, T.A., Brissett, N.C., Ehlinger, A., Keen, B.A., Kolesar, P., Taylor, E.M., Bailey, L.J., Lindsay, H.D., Chazin, W.J., Doherty, A.J.

(2017) Nat Commun 8: 15222-15222

• PubMed: 28534480 
• DOI: https://doi.org/10.1038/ncomms15222
• Primary Citation Related Structures: 
  5N85, 5N8A


• PubMed Abstract: 
  

  DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multifunctional replicative enzyme called primase-polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA. Using biophysical and crystallographic approaches, we identify that PrimPol possesses two RPA-binding motifs and ascertained the key residues required for these interactions. We demonstrate that one of these motifs is critical for PrimPol's recruitment to stalled replication forks in vivo. In addition, biochemical analysis reveals that RPA serves to stimulate the primase activity of PrimPol. Together, these findings provide significant molecular insights into PrimPol's mode of recruitment to stalled forks to facilitate repriming and restart.

---

Organizational Affiliation: 
• Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering, isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 24.52 kDa 
• Atom Count: 1,200 
• Modeled Residue Count: 130 
• Deposited Residue Count: 223 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed primase/polymerase protein	A [auth X]	102	Homo sapiens	Mutation(s): 0  Gene Names: PRIMPOL, CCDC111 EC: 2.7.7 (PDB Primary Data), 2.7.7.102 (UniProt), 2.7.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LW4 (Homo sapiens) Explore Q96LW4  Go to UniProtKB:  Q96LW4
PHAROS:  Q96LW4 GTEx:  ENSG00000164306

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 70 kDa DNA-binding subunit	B [auth A]	121	Homo sapiens	Mutation(s): 1  Gene Names: RPA1, REPA1, RPA70
UniProt & NIH Common Fund Data Resources
Find proteins for P27694 (Homo sapiens) Explore P27694  Go to UniProtKB:  P27694
PHAROS:  P27694 GTEx:  ENSG00000132383

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.05	α = 90
b = 53.49	β = 90
c = 53.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Brissett, N.C., Doherty, A.J.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/H019723/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M008800/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M004236/1

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description