5Y18 | pdb_00005y18

Crystal structure of DAXX helical bundle domain in complex with ATRX

• PDB DOI: https://doi.org/10.2210/pdb5Y18/pdb

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


• Deposited: 2017-07-19 Released: 2018-05-30 
• Deposition Author(s): Chen, Y., Wang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Structural basis for DAXX interaction with ATRX

Wang, X., Zhao, Y., Zhang, J., Chen, Y.

(2017) Protein Cell 8: 767-771

• PubMed: 28875424 
• DOI: https://doi.org/10.1007/s13238-017-0462-y
• Primary Citation of Related Structures:  
  5Y18

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.68 kDa 
• Atom Count: 866 
• Modeled Residue Count: 102 
• Deposited Residue Count: 118 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death domain-associated protein 6	A	95	Homo sapiens	Mutation(s): 0  Gene Names: DAXX, BING2, DAP6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UER7 (Homo sapiens) Explore Q9UER7  Go to UniProtKB:  Q9UER7
PHAROS:  Q9UER7 GTEx:  ENSG00000204209

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator ATRX	B	23	Homo sapiens	Mutation(s): 0  Gene Names: ATRX, RAD54L, XH2 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P46100 (Homo sapiens) Explore P46100  Go to UniProtKB:  P46100
PHAROS:  P46100 GTEx:  ENSG00000085224

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.485	α = 90
b = 107.904	β = 90
c = 30.887	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
SHARP	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Chen, Y., Wang, X.

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary