4OO6 | pdb_00004oo6

Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma protein 1)

PDB DOI: https://doi.org/10.2210/pdb4OO6/pdb

Classification: Transport Protein/RNA Binding Protein
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-30 Released: 2014-02-12
Deposition Author(s): Sampathkumar, P., Brower, A., Soniat, M., Bonanno, J., Hillerich, B., Seidel, R.D., Rout, M.P., Chook, Y.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.238 (Depositor), 0.203 (DCC)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma protein 1)

Sampathkumar, P., Brower, A., Soniat, M., Bonanno, J., Hillerich, B., Seidel, R.D., Rout, M.P., Chook, Y.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 100.35 kDa
Atom Count: 6,753
Modeled Residue Count: 844
Deposited Residue Count: 881
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transportin-1	A	854	Homo sapiens	Mutation(s): 0 Gene Names: KPNB2, MIP1, TNPO1, TRN
UniProt & NIH Common Fund Data Resources
Find proteins for Q92973 (Homo sapiens) Explore Q92973 Go to UniProtKB: Q92973
PHAROS: Q92973 GTEx: ENSG00000083312
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92973
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 39	B	27	Homo sapiens	Mutation(s): 0 Gene Names: HCC1, RBM39, RNPC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14498 (Homo sapiens) Explore Q14498 Go to UniProtKB: Q14498
PHAROS: Q14498 GTEx: ENSG00000131051
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14498
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.238 (Depositor), 0.203 (DCC)
R-Value Work: 0.189 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.584	α = 90
b = 162.152	β = 90
c = 68.501	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-02-12

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)

Revision History (Full details and data files)

Version 1.0: 2014-02-12
Type: Initial release
Version 1.1: 2017-07-26
Changes: Source and taxonomy
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description