9O6B | pdb_00009o6b

X-Ray structure of F240L mutant HOXB13 in complex with DNA (CAA)

PDB DOI: https://doi.org/10.2210/pdb9O6B/pdb
NAKB: 9O6B

Classification: TRANSCRIPTION
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2025-04-11 Released: 2026-04-15
Deposition Author(s): Dikbas, U.M., Wong, J.T., Chen, Y.S., Lallous, N., Van Petegem, F., Lack, N.A.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.273 (Depositor), 0.264 (DCC)
R-Value Work:
0.226 (Depositor), 0.218 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of HOXB13 Homeobox Domain Germline Mutations Driving Prostate Cancer

Dikbas, U.M., Wong, J.T., Chen, Y.S., Lallous, N., Van Petegem, F., Lack, N.A.

To be published.

Macromolecule Content

Total Structure Weight: 45.29 kDa
Atom Count: 2,551
Modeled Residue Count: 194
Deposited Residue Count: 274
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Hox-B13	A [auth J], D [auth A]	101	Homo sapiens	Mutation(s): 1 Gene Names: HOXB13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92826 (Homo sapiens) Explore Q92826 Go to UniProtKB: Q92826
PHAROS: Q92826 GTEx: ENSG00000159184
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92826
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA-TTGTGTTTTATTGGGTCC	B [auth K], E [auth B]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA-GGACCCAATAAAACACAA	C [auth L], F [auth C]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.273 (Depositor), 0.264 (DCC)
R-Value Work: 0.226 (Depositor), 0.218 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.22	α = 90
b = 57.82	β = 119
c = 75.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Van Petegem, F.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	202003PJT-437633

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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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.