7PSX | pdb_00007psx

Structure of HOXB13 bound to hydroxymethylated DNA

• PDB DOI: https://doi.org/10.2210/pdb7PSX/pdb
• NAKB: 7PSX

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


• Deposited: 2021-09-24 Released: 2022-10-05 
• 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: 2.00 Å
• R-Value Free: 
  0.283 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Structure of HOXB13 bound to hydroxymethylated DNA

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.94 kDa 
• Atom Count: 5,413 
• Modeled Residue Count: 383 
• Deposited Residue Count: 388 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Hox-B13	A, D [auth B], G, J	61	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: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')	B [auth C], E [auth D], H, K	18	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')	C [auth F], F [auth E], I, L	18	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	M [auth C], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.283 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.153	α = 88.02
b = 55.541	β = 81.46
c = 101.08	γ = 84.94

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
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: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description