9WVH | pdb_00009wvh

Crystal structure of TONSL UBL domain

PDB DOI: https://doi.org/10.2210/pdb9WVH/pdb

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-20 Released: 2025-10-08
Deposition Author(s): Karmakar, A., Roy, S.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.209 (Depositor), 0.219 (DCC)
R-Value Work:
0.194 (Depositor), 0.204 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of TONSL UBL domain

Karmakar, A., Roy, S.

To be published.

Macromolecule Content

Total Structure Weight: 19.56 kDa
Atom Count: 1,378
Modeled Residue Count: 159
Deposited Residue Count: 170
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tonsoku-like protein	A, B	85	Homo sapiens	Mutation(s): 0 Gene Names: TONSL, IKBR, NFKBIL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HA7 (Homo sapiens) Explore Q96HA7 Go to UniProtKB: Q96HA7
PHAROS: Q96HA7 GTEx: ENSG00000160949
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96HA7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.209 (Depositor), 0.219 (DCC)
R-Value Work: 0.194 (Depositor), 0.204 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.147	α = 90
b = 112.147	β = 90
c = 69.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	CRG/2022/001895

Revision History (Full details and data files)

Version 1.0: 2025-10-08
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.