1YN6

Crystal structure of a mouse MHC class I protein, H2-Db, in complex with a peptide from the influenza A acid polymerase

PDB DOI: https://doi.org/10.2210/pdb1YN6/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Influenza A virus (strain A/Swine/Iowa/15/1930 H1N1)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-01-23 Released: 2005-06-28
Deposition Author(s): Turner, S.J., Kedzierska, K., Komodromou, H., La Gruta, N.L., Dunstone, M.A., Webb, A.I., Webby, R., Walden, H., Xie, W., McCluskey, J., Purcell, A.W., Rossjohn, J., Doherty, P.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254
R-Value Work: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Lack of prominent peptide-major histocompatibility complex features limits repertoire diversity in virus-specific CD8+ T cell populations

Turner, S.J., Kedzierska, K., Komodromou, H., La Gruta, N.L., Dunstone, M.A., Webb, A.I., Webby, R., Walden, H., Xie, W., McCluskey, J., Purcell, A.W., Rossjohn, J., Doherty, P.C.

(2005) Nat Immunol 6: 382-389

PubMed: 15785764 Search on PubMed
DOI: https://doi.org/10.1038/ni0405-365
Primary Citation of Related Structures:
1YN6, 1YN7

Macromolecule Content

Total Structure Weight: 44.83 kDa
Atom Count: 3,512
Modelled Residue Count: 383
Deposited Residue Count: 383
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A	273	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01899 (Mus musculus) Explore P01899 Go to UniProtKB: P01899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01899
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Mus musculus	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
10-mer peptide from RNA-directed RNA polymerase subunit P2	C	10	N/A	Mutation(s): 0 EC: 2.7.7.48 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P13175 (Influenza A virus (strain A/Swine/Iowa/15/1930 H1N1)) Explore P13175 Go to UniProtKB: P13175
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13175
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254
R-Value Work: 0.209
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.216	α = 90
b = 56.216	β = 90
c = 273.504	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-06-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-06-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary