4D2G

Crystal structure of human PCNA in complex with p15 peptide

• PDB DOI:  https://doi.org/10.2210/pdb4D2G/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-09 Released: 2015-03-18 
• Deposition Author(s): DeBiasio, A., Ibanez, A., Mortuza, G., Molina, R., Cordeiro, T.N., Castillo, F., Villate, M., Merino, N., Lelli, M., Diercks, T., Luque, I., Bernardo, P., Montoya, G., Blanco, F.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.250 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 

Literature

Structure of P15(Paf)-PCNA Complex and Implications for Clamp Sliding During DNA Replication and Repair.

De Biasio, A., De Opakua, A.I., Mortuza, G.B., Molina, R., Cordeiro, T.N., Castillo, F., Villate, M., Merino, N., Delgado, S., Gil-Carton, D., Luque, I., Diercks, T., Bernado, P., Montoya, G., Blanco, F.J.

(2015) Nat Commun 6: 6439

• PubMed: 25762514 
• DOI: https://doi.org/10.1038/ncomms7439
• Primary Citation of Related Structures:  
  4D2G


• PubMed Abstract: 
  

The intrinsically disordered protein p15(PAF) regulates DNA replication and repair by binding to the proliferating cell nuclear antigen (PCNA) sliding clamp. We present the structure of the human p15(PAF)-PCNA complex. Crystallography and NMR show the central PCNA-interacting protein motif (PIP-box) of p15(PAF) tightly bound to the front-face of PCNA. In contrast to other PCNA-interacting proteins, p15(PAF) also contacts the inside of, and passes through, the PCNA ring. The disordered p15(PAF) termini emerge at opposite faces of the ring, but remain protected from 20S proteasomal degradation. Both free and PCNA-bound p15(PAF) binds DNA mainly through its histone-like N-terminal tail, while PCNA does not, and a model of the ternary complex with DNA inside the PCNA ring is consistent with electron micrographs. We propose that p15(PAF) acts as a flexible drag that regulates PCNA sliding along the DNA and facilitates the switch from replicative to translesion synthesis polymerase binding.

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Organizational Affiliation: 

1] Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain [2] IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 91.88 kDa 
• Atom Count: 6,461 
• Modelled Residue Count: 814 
• Deposited Residue Count: 834 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROLIFERATING CELL NUCLEAR ANTIGEN	A, B, C	264	Homo sapiens	Mutation(s): 0  Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens) Explore P12004  Go to UniProtKB:  P12004
PHAROS:  P12004

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P15	D, E	21	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15004 (Homo sapiens) Explore Q15004  Go to UniProtKB:  Q15004
PHAROS:  Q15004

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.250 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.053	α = 90
b = 41.228	β = 105.39
c = 141.121	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): DeBiasio, A., Ibanez, A., Mortuza, G., Molina, R., Cordeiro, T.N., Castillo, F., Villate, M., Merino, N., Lelli, M., Diercks, T., Luque, I., Bernardo, P., Montoya, G., Blanco, F.J.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2015-03-25
  Changes: Database references