8BYX

HOXB13-homodimer bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb8BYX/pdb
• NAKB: 8BYX

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


• Deposited: 2022-12-14 Released: 2023-12-27 
• Deposition Author(s): Morgunova, E., Popov, A., Yin, Y., Taipale, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.304 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 

Literature

HOXB13-homodimer bound to DNA

Morgunova, E., Popov, A., Yin, Y., Taipale, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.5 kDa 
• Atom Count: 5,225 
• Modelled Residue Count: 461 
• Deposited Residue Count: 486 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Hox-B13	C [auth B], F [auth A], I [auth G], J, K, L	63	Homo sapiens	Mutation(s): 0  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 ID: 1
Molecule	Chains	Length	Organism	Image
DNA	A [auth D], D [auth C], G [auth H]	18	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B [auth E], E [auth F], H [auth I]	18	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.304 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.779	α = 90
b = 116.779	β = 90
c = 118.057	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Morgunova, E., Popov, A., Yin, Y., Taipale, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release