5EG0

HOXB13-MEIS1 heterodimer bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb5EG0/pdb
• NAKB: 5EG0

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


• Deposited: 2015-10-26 Released: 2016-11-09 
• Deposition Author(s): Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.322 
• R-Value Work: 0.285 
• R-Value Observed: 0.288 

Starting Model: experimental

Literature

Molecular basis of recognition of two distinct DNA sequences by a single transcription factor

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 25.12 kDa 
• Atom Count: 1,743 
• Modelled Residue Count: 153 
• Deposited Residue Count: 154 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Meis2	A	57	Homo sapiens	Mutation(s): 0  Gene Names: MEIS2, MRG1
UniProt & NIH Common Fund Data Resources
Find proteins for O14770 (Homo sapiens) Explore O14770  Go to UniProtKB:  O14770
PHAROS:  O14770 GTEx:  ENSG00000134138

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Hox-B13	D [auth B]	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*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*G)-3')	B [auth D]	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')	C [auth E]	18	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.322 
• R-Value Work: 0.285 
• R-Value Observed: 0.288 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.726	α = 90
b = 56.332	β = 90
c = 115.152	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description