6G9Q | pdb_00006g9q

Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen derived from dopamine monooxygenase.

• PDB DOI: https://doi.org/10.2210/pdb6G9Q/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-04-11 Released: 2019-04-24 
• Deposition Author(s): Achour, A., Sandalova, T., Allerbring, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structural basis for CD8+ T cells auto-reactivity in LCMV infection

Allerbring, E., Duru, A.D., Nygren, P.A., Sandalova, T., Achour, A.

To be published.

Biological Assembly 1  

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: 96.71 kDa 
• Atom Count: 6,675 
• Modelled Residue Count: 808 
• Deposited Residue Count: 847 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A	276	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus) Explore P01899  Go to UniProtKB:  P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	119	Mus musculus	Mutation(s): 1  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha variable 14-1,T-cell receptor alpha chain C region	C [auth G]	205	Mus musculus	Mutation(s): 0  Gene Names: Trav14-1, Tcra
UniProt
Find proteins for A0A0G2JF94 (Mus musculus) Explore A0A0G2JF94  Go to UniProtKB:  A0A0G2JF94

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta chain V region C5,T-cell receptor beta-1 chain C region	D [auth H]	238	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P04213 (Mus musculus) Explore P04213  Go to UniProtKB:  P04213
Find proteins for P01852 (Mus musculus) Explore P01852  Go to UniProtKB:  P01852
UniProt Groups	P01852P04213

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Dopamine beta-hydroxylase	E [auth P]	9	Mus musculus	Mutation(s): 1  EC: 1.14.17.1
UniProt
Find proteins for Q64237 (Mus musculus) Explore Q64237  Go to UniProtKB:  Q64237

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 256.383	α = 90
b = 46.622	β = 94.2
c = 90.059	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Achour, A., Sandalova, T., Allerbring, E.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary