1TMC | pdb_00001tmc

THE THREE-DIMENSIONAL STRUCTURE OF A CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE MISSING THE ALPHA3 DOMAIN OF THE HEAVY CHAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.207 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain.

Collins, E.J.Garboczi, D.N.Karpusas, M.N.Wiley, D.C.

(1995) Proc Natl Acad Sci U S A 92: 1218-1221

  • DOI: https://doi.org/10.1073/pnas.92.4.1218
  • Primary Citation Related Structures: 
    1TMC

  • PubMed Abstract: 

    Class I major histocompatibility complex (MHC) molecules are ternary complexes of the soluble serum protein beta 2-microglobulin, MHC heavy chain, and bound peptide. The first two domains (alpha 1, alpha 2) of the heavy chain create the peptide binding cleft and the surface that contacts the T-cell receptor. The third domain (alpha 3) associates with the T-cell co-receptor, CD8, during T-cell recognition. Here we describe the x-ray crystal structure of a human class I MHC molecule, HLA-Aw68, from which the alpha 3 domain has been proteolytically removed. The resulting molecule shows no gross morphological changes compared to the intact protein. A decameric peptide complexed with the intact HLA-Aw68 is seen to bind to the proteolized molecule in the conventional manner, demonstrating that the alpha 3 domain is not required for the structural integrity of the molecule or for peptide binding.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138.

Macromolecule Content 

  • Total Structure Weight: 33.42 kDa 
  • Atom Count: 2,439 
  • Modeled Residue Count: 284 
  • Deposited Residue Count: 285 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-AW68)175Homo sapiensMutation(s): 0 
Gene Names: BETA-2-MICROGLOBULIN
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA 2-MICROGLOBULIN100Homo sapiensMutation(s): 0 
Gene Names: BETA-2-MICROGLOBULIN
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DECAMERIC PEPTIDE (EVAPPEYHRK)10N/AMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.207 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.23α = 90
b = 58.05β = 90
c = 109.53γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-10-30
    Changes: Structure summary