3HUP

High-resolution structure of the extracellular domain of human CD69

• PDB DOI: https://doi.org/10.2210/pdb3HUP/pdb

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


• Deposited: 2009-06-15 Released: 2009-12-15 
• Deposition Author(s): Kolenko, P., Dohnalek, J., Skalova, T., Hasek, J., Duskova, J., Vanek, O., Bezouska, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.184 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Literature

The high-resolution structure of the extracellular domain of human CD69 using a novel polymer

Kolenko, P., Skalova, T., Vanek, O., Stepankova, A., Duskova, J., Hasek, J., Bezouska, K., Dohnalek, J.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1258-1260

• PubMed: 20054122 
• DOI: https://doi.org/10.1107/S1744309109043152
• Primary Citation of Related Structures:  
  3HUP


• PubMed Abstract: 
  

  The structure of the extracellular domain of human CD69 has been determined by single-crystal X-ray diffraction. The structure refined to 1.37 A resolution provides further details of the overall structure and the asymmetric interface between the monomers in the native dimer. The protein was crystallized using di[poly(ethylene glycol)] adipate, which also served as a cryoprotectant. This is the first report of a crystal structure determined using crystals grown with this polymer.

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Organizational Affiliation: 

Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2/1888, 162 06 Praha 6, Czech Republic. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 30.49 kDa 
• Atom Count: 2,387 
• Modelled Residue Count: 239 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Early activation antigen CD69	A, B	130	Homo sapiens	Mutation(s): 0  Gene Names: CD69
UniProt & NIH Common Fund Data Resources
Find proteins for Q07108 (Homo sapiens) Explore Q07108  Go to UniProtKB:  Q07108
PHAROS:  Q07108 GTEx:  ENSG00000110848

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.184 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.067	α = 90
b = 86.067	β = 90
c = 61.975	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Kolenko, P., Dohnalek, J., Skalova, T., Hasek, J., Duskova, J., Vanek, O., Bezouska, K.

Revision History  

• Version 1.0: 2009-12-15
  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