4RU2 | pdb_00004ru2

Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb4RU2/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-11-17 Released: 2015-02-04
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.204 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.190 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

To be published.

Macromolecule Content

Total Structure Weight: 144.55 kDa
Atom Count: 9,172
Modeled Residue Count: 1,098
Deposited Residue Count: 1,287
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 39 (RBM39)	A, C, E, G, I A, C, E, G, I, K, M, O, Q	114	Mus musculus	Mutation(s): 1 Gene Names: CAPER, RBM39, RNPC2, WS20613E
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VH51 (Mus musculus) Explore Q8VH51 Go to UniProtKB: Q8VH51
IMPC: MGI:2157953
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VH51
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor U2AF 65 kDa subunit	B, D, F, H, J B, D, F, H, J, L, N, P, R	29	Mus musculus	Mutation(s): 0 Gene Names: U2AF2, U2AF65, WT4514D
UniProt & NIH Common Fund Data Resources
Find proteins for P26369 (Mus musculus) Explore P26369 Go to UniProtKB: P26369
IMPC: MGI:98886
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26369
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.204 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.190 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34RU2

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.283	α = 90
b = 127.283	β = 90
c = 78.864	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-02-04

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Partnership for T-Cell Biology (TCELL)

Revision History (Full details and data files)

Version 1.0: 2015-02-04
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-02-01
Changes: Database references
Version 1.3: 2023-09-20
Changes: Data collection, Refinement description

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.