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

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62987
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12888
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Funding Organization	Location	Grant Number
CIHR Foundation Grant	Canada	FDN 143277

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.