4LIR | pdb_00004lir

Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution

PDB DOI: https://doi.org/10.2210/pdb4LIR/pdb

Classification: TRANSPORT PROTEIN, NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-03 Released: 2013-09-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 26.27 kDa
Atom Count: 1,286
Modeled Residue Count: 164
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP53	A, B	117	Homo sapiens	Mutation(s): 0 Gene Names: BC047029, MP44, NUP35, NUP53
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH5 (Homo sapiens) Explore Q8NFH5 Go to UniProtKB: Q8NFH5
PHAROS: Q8NFH5 GTEx: ENSG00000163002
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NFH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34LIR

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.59	α = 90
b = 70.59	β = 90
c = 160.19	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: 2013-09-11

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: 2013-09-11
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
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.