5TIL | pdb_00005til

Murine class I major histocompatibility complex H-2 Db in complex with LCMV-derived GP33 altered peptide V3P and T-cell receptor P14

PDB DOI: https://doi.org/10.2210/pdb5TIL/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: 2017-11-01
Deposition Author(s): Achour, A., Sandalova, T., Allerbring, E.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.275 (Depositor), 0.276 (DCC)
R-Value Work:
0.219 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5TIL

This is version 1.1 of the entry. See complete history.

Literature

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

Allerbring, E., Duru, A.D., Sun, R., Han, X., Uchtenhagen, H., Madhurantakam, C., Popov, A., Markoba, N., Talyzina, A., Nygren, P.A., Sandalova, T., Achour, A.

To be published.

Macromolecule Content

Total Structure Weight: 184.13 kDa
Atom Count: 11,851
Modeled Residue Count: 1,462
Deposited Residue Count: 1,609
Unique protein chains: 6

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A, D	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

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	99	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	C, F	9	Mammarenavirus choriomeningitidis	Mutation(s): 2
UniProt
Find proteins for Q9QDK7 (Mammarenavirus choriomeningitidis) Explore Q9QDK7 Go to UniProtKB: Q9QDK7
Entity Groups
UniProt Group	Q9QDK7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha chain of P14 T cell receptor	G	205	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta chain of murine T cell receptor P14	H, J [auth L]	238	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha chain of murine P14 T cell receptor	I [auth K]	160	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.275 (Depositor), 0.276 (DCC)
R-Value Work: 0.219 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.224	α = 90
b = 66.698	β = 90
c = 523.485	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-11-01

Deposition Author(s):

Allerbring, E.B.

Revision History (Full details and data files)

Version 1.0: 2017-11-01
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.