9NIB | pdb_00009nib

Black sea bass polyomavirus LTA NLS bound to improtin alpha 2

PDB DOI: https://doi.org/10.2210/pdb9NIB/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Mus musculus, Black sea bass polyomavirus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-02-25 Released: 2026-04-01
Deposition Author(s): Hoad, M., Forwood, J.K., Alvisi, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Positioning of Nuclear Localization Signals as an Evolutionary Marker in Polyomavirus Large Tumor Antigens

Hoad, M., Pavan, S., Nematollahzadeh, S., Tietz, O., Reeman, J., Forwood, J.K., Alvisi, G.

To be published.

Macromolecule Content

Total Structure Weight: 58.18 kDa
Atom Count: 3,430
Modeled Residue Count: 436
Deposited Residue Count: 534
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin subunit alpha-1	A	510	Mus musculus	Mutation(s): 0 Gene Names: Kpna2, Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus) Explore P52293 Go to UniProtKB: P52293
IMPC: MGI:103561
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52293
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Truncated large T antigen	B	24	Black sea bass polyomavirus 1	Mutation(s): 0 EC: 5.6.2.4
UniProt
Find proteins for A0A0A1C723 (black sea bass-associated polyomavirus 1) Explore A0A0A1C723 Go to UniProtKB: A0A0A1C723
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A1C723
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.802	α = 90
b = 89.188	β = 90
c = 99.659	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-04-01
Type: Initial release

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.