Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

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

Macromolecule Content

• Total Structure Weight: 98356.16 
• Atom Count: 6433 
• Residue Count: 870 
• Unique protein chains: 4

3PL6

Structure of Autoimmune TCR Hy.1B11 in complex with HLA-DQ1 and MBP 85-99

• DOI: 10.2210/pdb3PL6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus


• Deposited: 2010-11-13 Released: 2010-12-22 
• Deposition Author(s): Sethi, D.K., Wucherpfennig, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.258 
• R-Value Work: 0.232 

Literature

A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC.

Sethi, D.K., Schubert, D.A., Anders, A.K., Heroux, A., Bonsor, D.A., Thomas, C.P., Sundberg, E.J., Pyrdol, J., Wucherpfennig, K.W.

(2011) J.Exp.Med. 208: 91-102

• PubMed: 21199956 
• DOI: 10.1084/jem.20100725


• PubMed Abstract: 
  

Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-α chain with the MHC class II β chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3β loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3α loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.

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Organizational Affiliation: 

Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MHC class II HLA-DQ-alpha chain	A	194	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQA1
Find proteins for A0A173ADG5 (Homo sapiens) Go to Gene View: HLA-DQA1 Go to UniProtKB:  A0A173ADG5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
MHC class II HLA-DQ-beta chain	B	202	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQB1
Find proteins for A0A0A8WFP6 (Homo sapiens) Go to Gene View: HLA-DQB1 Go to UniProtKB:  A0A0A8WFP6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
T-cell receptor alpha chain	C	206	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
MBP peptide / T-cell receptor beta chain chimera	D	268	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.258 
• R-Value Work: 0.232 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 73.123	α = 90.00
b = 124.815	β = 90.00
c = 134.921	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-13 
• Released Date: 2010-12-22 
• Deposition Author(s): Sethi, D.K., Wucherpfennig, K.W.

Revision History 

• Version 1.0: 2010-12-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-07-26
  Type: Source and taxonomy
• Version 1.3: 2017-11-08
  Type: Refinement description