5M02 | pdb_00005m02

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

PDB DOI: https://doi.org/10.2210/pdb5M02/pdb

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

Deposited: 2016-10-03 Released: 2017-12-20
Deposition Author(s): Achour, A., Sandalova, T., Sun, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.214 (Depositor), 0.221 (DCC)
R-Value Work:
0.188 (Depositor), 0.197 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 96.91 kDa
Atom Count: 6,998
Modeled Residue Count: 809
Deposited Residue Count: 847
Unique protein chains: 5

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01899
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 A0A0G2JF94 (Mus musculus) Explore A0A0G2JF94 Go to UniProtKB: A0A0G2JF94
Find proteins for P01849 (Mus musculus) Explore P01849 Go to UniProtKB: P01849
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A0G2JF94 P01849
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 P01851 (Mus musculus) Explore P01851 Go to UniProtKB: P01851
Find proteins for P04213 (Mus musculus) Explore P04213 Go to UniProtKB: P04213
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P04213 P01851
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H	F [auth A], G [auth A], H	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.214 (Depositor), 0.221 (DCC)
R-Value Work: 0.188 (Depositor), 0.197 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 255.11	α = 90
b = 46.5	β = 94.6
c = 89.02	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Achour, A.

Sandalova, T.

Sun, R.

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary