Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 97.41 kDa 
• Atom Count: 6908 
• Modelled Residue Count: 812 
• Deposited Residue Count: 844 
• Unique protein chains: 5

1J8H

Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA Antigen Peptide, and MHC Class II Molecule, HLA-DR4

• DOI: 10.2210/pdb1J8H/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Alphainfluenzavirus
• Expression System: Drosophila melanogaster, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-05-21 Released: 2002-03-13 
• Deposition Author(s): Hennecke, J., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.211 

Literature

Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity.

Hennecke, J., Wiley, D.C.

(2002) J Exp Med 195: 571-581

• PubMed: 11877480 
• DOI: 10.1084/jem.20011194
• Primary Citation of Related Structures:  
  1J8H


• PubMed Abstract: 
  

The alpha/beta T cell receptor (TCR) HA1.7 specific for the hemagglutinin (HA) antigen peptide from influenza A virus is HLA-DR1 restricted but cross-reactive for the HA peptide presented by the allo-major histocompatibility complex (MHC) class II molecule HLA-DR4. We report here the structure of the HA1.7/DR4/HA complex, determined by X-ray crystallography at a resolution of 2.4 A. The overall structure of this complex is very similar to the previously reported structure of the HA1.7/DR1/HA complex. Amino acid sequence differences between DR1 and DR4, which are located deep in the peptide binding groove and out of reach for direct contact by the TCR, are able to indirectly influence the antigenicity of the pMHC surface by changing the conformation of HA peptide residues at position P5 and P6. Although TCR HA1.7 is cross-reactive for HA presented by DR1 and DR4 and tolerates these conformational differences, other HA-specific TCRs are sensitive to these changes. We also find a dependence of the width of the MHC class II peptide-binding groove on the sequence of the bound peptide by comparing the HA1.7/DR4/HA complex with the structure of DR4 presenting a collagen peptide. This structural study of TCR cross-reactivity emphasizes how MHC sequence differences can affect TCR binding indirectly by moving peptide atoms.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN	A	181	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-4 BETA CHAIN	B	192	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ HA1 PEPTIDE CHAIN	C	13	Alphainfluenzavirus	Mutation(s): 0
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437  Go to UniProtKB:  P03437

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR ALPHA CHAIN	D	212	Homo sapiens	Mutation(s): 0  Gene Names: TRAC, TCRA
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS:  P01848

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR BETA CHAIN	E	246	Homo sapiens	Mutation(s): 1  Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.753	α = 90
b = 73.317	β = 108.52
c = 123.033	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-21 
• Released Date: 2002-03-13 
Deposition Author(s): Hennecke, J., Wiley, D.C.

Revision History  

• Version 1.0: 2002-03-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary