4NSK | pdb_00004nsk

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand V3P

PDB DOI: https://doi.org/10.2210/pdb4NSK/pdb
Entry: 4NSK supersedes: 3TBX

Classification: Immune system/peptide
Organism(s): Mus musculus, Lymphocytic choriomeningitis virus (strain WE)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-11-28 Released: 2014-01-01
Deposition Author(s): Allerbring, E.B., Duru, A.D., Uchtenhagen, H., Mazumdar, P.A., Badia-Martinez, D., Madhurantakam, C., Sandalova, T., Nygren, P., Achour, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.283 (Depositor), 0.283 (DCC)
R-Value Work:
0.216 (Depositor), 0.218 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand V3P

Allerbring, E.B., Duru, A.D., Uchtenhagen, H., Mazumdar, P.A., Badia-Martinez, D., Madhurantakam, C., Sandalova, T., Nygren, P., Achour, A.

To be published.

Macromolecule Content

Total Structure Weight: 44.84 kDa
Atom Count: 3,187
Modeled Residue Count: 382
Deposited Residue Count: 384
Unique protein chains: 3

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	99	Mus musculus	Mutation(s): 0 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	C	9	N/A	Mutation(s): 0
UniProt
Find proteins for P07399 (Lymphocytic choriomeningitis virus (strain WE)) Explore P07399 Go to UniProtKB: P07399
Entity Groups
UniProt Group	P07399
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.283 (Depositor), 0.283 (DCC)
R-Value Work: 0.216 (Depositor), 0.218 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.46	α = 90
b = 108.54	β = 122.43
c = 57.39	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-01

Deposition Author(s):

This entry supersedes: 3TBX

Revision History (Full details and data files)

Version 1.0: 2014-01-01
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-27
Changes: Structure summary