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RCSB PDB
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Computed Structure Models (CSM)
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 1E8I|pdb_00001e8i

HUMAN CD69 - TETRAGONAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.270 (Depositor) 
  • R-Value Work: 
    0.248 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the C-Type Lectin-Like Domain from the Human Hematopoietic Cell Receptor Cd69

Llera, A.S.Viedma, F.Sanchez-Madrid, F.Tormo, J.

(2001) J Biological Chem 276: 7312

  • PubMed11036086 Search on PubMed
  • DOI: https://doi.org/10.1074/jbc.M008573200
  • Primary Citation of Related Structures:  
    1E87,1E8I

  • PubMed Abstract: 

    CD69, one of the earliest specific antigens acquired during lymphoid activation, acts as a signal-transducing receptor involved in cellular activation events, including proliferation and induction of specific genes. CD69 belongs to a family of receptors that modulate the immune response and whose genes are clustered in the natural killer (NK) gene complex. The extracellular portion of these receptors represent a subfamily of C-type lectin-like domains (CTLDs), which are divergent from true C-type lectins and are referred to as NK-cell domains (NKDs). We have determined the three-dimensional structure of human CD69 NKD in two different crystal forms. CD69 NKD adopts the canonical CTLD fold but lacks the features involved in Ca(2+) and carbohydrate binding by C-type lectins. CD69 NKD dimerizes noncovalently, both in solution and in crystalline state. The dimer interface consists of a hydrophobic, loosely packed core, surrounded by polar interactions, including an interdomain beta sheet. The intersubunit core shows certain structural plasticity that may facilitate conformational rearrangements for binding to ligands. The surface equivalent to the binding site of other members of the CTLD superfamily reveals a hydrophobic patch surrounded by conserved charged residues that probably constitutes the CD69 ligand-binding site.


  • Organizational Affiliation
    • Department of Macromolecular Structure, Centro Nacional de Biotecnologia, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (SO4)


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


Find Similar Assemblies

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

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Macromolecule Content 

  • Total Structure Weight: 27.71 kDa 
  • Atom Count: 1,995 
  • Modeled Residue Count: 234 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EARLY ACTIVATION ANTIGEN CD69118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07108 (Homo sapiens)
Explore Q07108 
Go to UniProtKB:  Q07108
PHAROS:  Q07108
GTEx:  ENSG00000110848 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07108
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.270 (Depositor) 
  • R-Value Work: 0.248 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.629α = 90
b = 69.629β = 90
c = 118.588γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2000-09-26 
  • Deposition Author(s): Tormo, J.

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.


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