3UWT | pdb_00003uwt

Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 2.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb3UWT/pdb

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

Deposited: 2011-12-02 Released: 2012-01-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.240 (Depositor), 0.250 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 2.50 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 22.31 kDa
Atom Count: 1,540
Modeled Residue Count: 197
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(U)-binding-splicing factor PUF60	A	200	Homo sapiens	Mutation(s): 0 Gene Names: BC008875, FIR, PUF60, ROBPI, SIAHBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHX1 (Homo sapiens) Explore Q9UHX1 Go to UniProtKB: Q9UHX1
PHAROS: Q9UHX1 GTEx: ENSG00000179950
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.240 (Depositor), 0.250 (DCC)
R-Value Work: 0.203 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33UWT

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.173	α = 90
b = 64.173	β = 90
c = 80.337	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-01-11

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: 2012-01-11
Type: Initial release
Version 1.1: 2015-10-21
Changes: Structure summary
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, Structure summary

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.