1AO7 | pdb_00001ao7

COMPLEX BETWEEN HUMAN T-CELL RECEPTOR, VIRAL PEPTIDE (TAX), AND HLA-A 0201

• PDB DOI: https://doi.org/10.2210/pdb1AO7/pdb

• Classification: COMPLEX (MHC/VIRAL PEPTIDE/RECEPTOR)
• Organism(s): Homo sapiens, Human T-cell leukemia virus type I
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-07-21 Released: 1997-09-17 
• Deposition Author(s): Garboczi, D.N., Ghosh, P., Utz, U., Fan, Q.R., Biddison, W.E., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.320 (Depositor), 0.327 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Models: experimental

Literature

Structure of the complex between human T-cell receptor, viral peptide and HLA-A2.

Garboczi, D.N., Ghosh, P., Utz, U., Fan, Q.R., Biddison, W.E., Wiley, D.C.

(1996) Nature 384: 134-141

• PubMed: 8906788 
• DOI: https://doi.org/10.1038/384134a0
• Primary Citation Related Structures: 
  1AO7


• PubMed Abstract: 
  

  Recognition by a T-cell antigen receptor (TCR) of peptide complexed with a major histocompatibility complex (MHC) molecule occurs through variable loops in the TCR structure which bury almost all the available peptide and a much larger area of the MHC molecule. The TCR fits diagonally across the MHC peptide-binding site in a surface feature common to all class I and class II MHC molecules, providing evidence that the nature of binding is general. A broadly applicable binding mode has implications for the mechanism of repertoire selection and the magnitude of alloreactions.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.03 kDa 
• Atom Count: 5,711 
• Modeled Residue Count: 707 
• Deposited Residue Count: 833 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA-A 0201	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A 0201
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2 MICROGLOBULIN	B	100	Homo sapiens	Mutation(s): 0  Gene Names: V BETA 12.3 [BV13S1] - D BETA 2.1 - J BETA 2.1 -
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TAX PEPTIDE	C	9	Human T-cell leukemia virus type I	Mutation(s): 0
UniProt
Find proteins for P14079 (Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A)) Explore P14079  Go to UniProtKB:  P14079

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T CELL RECEPTOR ALPHA	D	204	Homo sapiens	Mutation(s): 0  Gene Names: V ALPHA 2.3 [AV2S1A2] - J ALPHA 24 - C ALPHA
UniProt & NIH Common Fund Data Resources
Find proteins for A0A075B6T6 (Homo sapiens) Explore A0A075B6T6  Go to UniProtKB:  A0A075B6T6
PHAROS:  A0A075B6T6 GTEx:  ENSG00000211789
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848
UniProt Groups	P01848A0A075B6T6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T CELL RECEPTOR BETA	E	245	Homo sapiens	Mutation(s): 0  Gene Names: V BETA 12.3 [BV13S1] - D BETA 2.1 - J BETA 2.1 - C BETA 2
UniProt
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	F [auth B], G [auth B]	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.320 (Depositor), 0.327 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.3	α = 90
b = 49.5	β = 89.6
c = 96	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
VECREF	model building
X-PLOR	model building
X-PLOR	refinement
VECREF	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-17 
Deposition Author(s): Garboczi, D.N., Ghosh, P., Utz, U., Fan, Q.R., Biddison, W.E., Wiley, D.C.

Revision History  

• Version 1.0: 1997-09-17
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2016-05-25
  Changes: Structure summary
• Version 1.6: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.7: 2024-11-20
  Changes: Data collection, Structure summary