5J26

Crystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant

• PDB DOI: https://doi.org/10.2210/pdb5J26/pdb

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


• Deposited: 2016-03-29 Released: 2016-12-14 
• Deposition Author(s): Wan, L., Canny, M., Juang, Y.C., Durocher, D., Sicheri, F.
• Funding Organization(s): CIHR Foundation Grant

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.287 
• R-Value Work: 0.231 
• R-Value Observed: 0.237 

Literature

A genetically encoded inhibitor of 53BP1 to stimulate homology-based gene editing

Wan, L., Canny, M., Juang, Y.C., Durocher, D., Sicheri, F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 21.8 kDa 
• Atom Count: 1,517 
• Modelled Residue Count: 190 
• Deposited Residue Count: 193 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin Variant i53	A [auth B]	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor suppressor p53-binding protein 1	B [auth A]	117	Homo sapiens	Mutation(s): 0  Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12888 (Homo sapiens) Explore Q12888  Go to UniProtKB:  Q12888
PHAROS:  Q12888 GTEx:  ENSG00000067369

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.287 
• R-Value Work: 0.231 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.531	α = 90
b = 47.768	β = 90
c = 94.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Wan, L., Canny, M., Juang, Y.C., Durocher, D., Sicheri, F.

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Funding Organization	Location	Grant Number
CIHR Foundation Grant	Canada	FDN 143277

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Data collection
• Version 1.2: 2017-09-27
  Changes: Data collection
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references