5E6I

Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2

Gao, M.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
Molecule Chains  Sequence Length Organism Details Image
TCR alpha chain,Human nkt tcr alpha chain A [auth G],
F [auth A],
K [auth F],
P		 208 Homo sapiens Mutation(s): 0 
UniProt
Find proteins for K7N5M3 (Homo sapiens)
Explore K7N5M3 
Go to UniProtKB:  K7N5M3
Entity Groups  
Sequence Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group K7N5M3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
Molecule Chains  Sequence Length Organism Details Image
T-cell receptor beta-2 chain C region B [auth H],
G [auth B],
L,
Q		 243 Homo sapiens Mutation(s): 0 
Gene Names: TRBC2
Entity Groups  
Sequence Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
Molecule Chains  Sequence Length Organism Details Image
HLA class I histocompatibility antigen, A-2 alpha chain C [auth I],
H [auth C],
M,
R		 276 Homo sapiens Mutation(s): 0 
Gene Names: HLA-A, HLAA
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 Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group P04439
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
Molecule Chains  Sequence Length Organism Details Image
Beta-2-microglobulin D [auth J],
I [auth D],
N,
S [auth U]		 100 Homo sapiens Mutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
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 Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group P61769
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
Molecule Chains  Sequence Length Organism Details Image
Matrix protein 1 E [auth K],
J [auth E],
O,
T		 9 Influenza A virus (A/Boston/2747243M/2009(H1N1)) Mutation(s): 0 
UniProt
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03485 
Go to UniProtKB:  P03485
Entity Groups  
UniProt Group P03485
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.263 
  • Space Group: P 1
Unit Cell:
Length ( Å ) Angle ( ˚ )
a = 71.853 α = 83.66
b = 123.614 β = 74.87
c = 139.036 γ = 73.17
Software Package:
Software Name Purpose
PHENIX refinement
d*TREK data scaling
PHASER phasing
Coot model building
PDB_EXTRACT data extraction
CrystalClear data reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding Organization Location Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States AI036900

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-29
    Changes: Derived calculations
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description