5M01

Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from LCMV

• PDB DOI: https://doi.org/10.2210/pdb5M01/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Mammarenavirus choriomeningitidis
• Expression System: Escherichia coli, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-10-03 Released: 2017-10-25 
• Deposition Author(s): Achour, A., Sandalova, T., Sun, R., Han, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant

Allerbring, E., Duru, A., Sun, R., Han, X., Uchtenhagen, H., Madhurantakam, C., Popov, A., Markova, N., Talyzina, A., 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: 96.74 kDa 
• Atom Count: 6,914 
• Modelled Residue Count: 811 
• 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
Protein Trav14-1,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 P01849 (Mus musculus) Explore P01849  Go to UniProtKB:  P01849
Find proteins for A0A0G2JF94 (Mus musculus) Explore A0A0G2JF94  Go to UniProtKB:  A0A0G2JF94
UniProt Groups	A0A0G2JF94P01849

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta chain V region C5,T-cell receptor beta-2 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 P01851 (Mus musculus) Explore P01851  Go to UniProtKB:  P01851
UniProt Groups	P04213P01851

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND PA	E [auth P]	9	Mammarenavirus choriomeningitidis	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 255.926	α = 90
b = 46.542	β = 94.34
c = 89.398	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: 2017-10-25 
Deposition Author(s): Achour, A., Sandalova, T., Sun, R., Han, X.

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary