Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.31 kDa 
• Atom Count: 6569 
• Residue Count: 820 
• Unique protein chains: 3

1L1O

Structure of the human Replication Protein A (RPA) trimerization core

• DOI: 10.2210/pdb1L1O/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-02-19 Released: 2002-06-05 
• Deposition Author(s): Bochkareva, E.V., Korolev, S., Lees-Miller, S.P., Bochkarev, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.282 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 

Literature

Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.

Bochkareva, E., Korolev, S., Lees-Miller, S.P., Bochkarev, A.

(2002) EMBO J 21: 1855-1863

• PubMed: 11927569 
• DOI: 10.1093/emboj/21.7.1855
• Primary Citation of Related Structures:  
  1L1O


• PubMed Abstract: 
  

The human single-stranded DNA-binding protein, replication protein A (RPA) binds DNA in at least two different modes: initial [8-10 nucleotides (nt)] and stable ( approximately 30 nt). Switching from 8 to 30 nt mode is associated with a large conformational change. Here we report the 2.8 A structure of the RPA trimerization core comprising the C-terminal DNA-binding domain of subunit RPA70 (DBD-C), the central DNA-binding domain of subunit RPA32 (DBD-D) and the entire RPA14 subunit. All three domains are built around a central oligonucleotide/oligosaccharide binding (OB)-fold and flanked by a helix at the C-terminus. Trimerization is mediated by three C-terminal helices arranged in parallel. The OB-fold of DBD-C possesses unique structural features; embedded zinc ribbon and helix-turn-helix motifs. Using time-resolved proteolysis with trypsin, we demonstrate that the trimerization core does not contribute to the binding with substrates of 10 nt, but interacts with oligonucleotides of 24 nt. Taken together, our data indicate that switching from 8-10 to 30 nt mode is mediated by DNA binding with the trimerization core.

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Related Citations: 

• The role for zinc in replication protein A.
  Bochkareva, E., Korolev, S., Bochkarev, A.
  (2000) J Biol Chem 275: 27332

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 14 kDa subunit	A, D	121	Homo sapiens	Mutation(s): 0  Gene Names: RFA3_HUMAN, RPA3, REPA3, RPA14
Find proteins for P35244 (Homo sapiens) Explore P35244  Go to UniProtKB:  P35244
NIH Common Fund Data Resources
PHAROS  P35244 GTEx  ENSG00000106399

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 32 kDa subunit	B, E	128	Homo sapiens	Mutation(s): 0  Gene Names: RFA2_HUMAN, RPA2, REPA2, RPA32, RPA34
Find proteins for P15927 (Homo sapiens) Explore P15927  Go to UniProtKB:  P15927
NIH Common Fund Data Resources
PHAROS  P15927 GTEx  ENSG00000117748

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 70 kDa DNA-binding subunit	C, F	181	Homo sapiens	Mutation(s): 0  Gene Names: RFA1_HUMAN, RPA1, REPA1, RPA70
Find proteins for P27694 (Homo sapiens) Explore P27694  Go to UniProtKB:  P27694
NIH Common Fund Data Resources
PHAROS  P27694 GTEx  ENSG00000132383

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C, F	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.282 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.527	α = 90
b = 88.527	β = 90
c = 341.09	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-19 
• Released Date: 2002-06-05 
Deposition Author(s): Bochkareva, E.V., Korolev, S., Lees-Miller, S.P., Bochkarev, A.

Revision History 

• Version 1.0: 2002-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance