3R45

Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP

• PDB DOI: https://doi.org/10.2210/pdb3R45/pdb

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


• Deposited: 2011-03-17 Released: 2011-04-06 
• Deposition Author(s): Hu, H., Liu, Y., Wang, M., Fang, J., Huang, H., Yang, N., Li, Y., Wang, J., Yao, X., Shi, Y., Li, G., Xu, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Structure of a CENP-A-histone H4 heterodimer in complex with chaperone HJURP

Hu, H., Liu, Y., Wang, M., Fang, J., Huang, H., Yang, N., Li, Y., Wang, J., Yao, X., Shi, Y., Li, G., Xu, R.M.

(2011) Genes Dev 25: 901-906

• PubMed: 21478274 
• DOI: https://doi.org/10.1101/gad.2045111
• Primary Citation of Related Structures:  
  3R45


• PubMed Abstract: 
  

  In higher eukaryotes, the centromere is epigenetically specified by the histone H3 variant Centromere Protein-A (CENP-A). Deposition of CENP-A to the centromere requires histone chaperone HJURP (Holliday junction recognition protein). The crystal structure of an HJURP-CENP-A-histone H4 complex shows that HJURP binds a CENP-A-H4 heterodimer. The C-terminal β-sheet domain of HJURP caps the DNA-binding region of the histone heterodimer, preventing it from spontaneous association with DNA. Our analysis also revealed a novel site in CENP-A that distinguishes it from histone H3 in its ability to bind HJURP. These findings provide key information for specific recognition of CENP-A and mechanistic insights into the process of centromeric chromatin assembly.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 40.4 kDa 
• Atom Count: 1,899 
• Modelled Residue Count: 217 
• Deposited Residue Count: 340 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3-like centromeric protein A	A	156	Homo sapiens	Mutation(s): 0  Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens) Explore P49450  Go to UniProtKB:  P49450
PHAROS:  P49450 GTEx:  ENSG00000115163

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	103	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction recognition protein	C	81	Homo sapiens	Mutation(s): 0  Gene Names: HJURP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCD3 (Homo sapiens) Explore Q8NCD3  Go to UniProtKB:  Q8NCD3
PHAROS:  Q8NCD3 GTEx:  ENSG00000123485

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], M [auth B], S [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 3 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.941	α = 90
b = 83.941	β = 90
c = 86.773	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Hu, H., Liu, Y., Wang, M., Fang, J., Huang, H., Yang, N., Li, Y., Wang, J., Yao, X., Shi, Y., Li, G., Xu, R.M.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-28
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description