3NAR

Crystal structure of ZHX1 HD4 (zinc-fingers and homeoboxes protein 1, homeodomain 4)

• PDB DOI: https://doi.org/10.2210/pdb3NAR/pdb

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


• Deposited: 2010-06-02 Released: 2010-07-07 
• Deposition Author(s): Ren, J., Bird, L.E., Owens, R.J., Stammers, D.K., Oxford Protein Production Facility (OPPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains

Bird, L.E., Ren, J., Nettleship, J.E., Folkers, G.E., Owens, R.J., Stammers, D.K.

(2010) BMC Struct Biol 10: 13-13

• PubMed: 20509910 
• DOI: https://doi.org/10.1186/1472-6807-10-13
• Primary Citation of Related Structures:  
  3NAR, 3NAU


• PubMed Abstract: 
  

  Zhx1 to 3 (zinc-fingers and homeoboxes) form a set of paralogous genes encoding multi-domain proteins. ZHX proteins consist of two zinc fingers followed by five homeodomains. ZHXs have biological roles in cell cycle control by acting as co-repressors of the transcriptional regulator Nuclear Factor Y. As part of a structural genomics project we have expressed single and multi-domain fragments of the different human ZHX genes for use in structure determination.

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Organizational Affiliation: 

University of Oxford, Headington, UK.

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)

Macromolecule Content

• Total Structure Weight: 22.24 kDa 
• Atom Count: 1,221 
• Modelled Residue Count: 140 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc fingers and homeoboxes protein 1	A, B	96	Homo sapiens	Mutation(s): 0  Gene Names: ZHX1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKY1 (Homo sapiens) Explore Q9UKY1  Go to UniProtKB:  Q9UKY1
PHAROS:  Q9UKY1 GTEx:  ENSG00000165156

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.9	α = 90
b = 48.8	β = 104.02
c = 49.32	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Ren, J., Bird, L.E., Owens, R.J., Stammers, D.K., Oxford Protein Production Facility (OPPF)

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description