1YN7 | pdb_00001yn7

Crystal structure of a mouse MHC class I protein, H2-Db, in complex with a mutated peptide (R7A) of the influenza A acid polymerase

• PDB DOI: https://doi.org/10.2210/pdb1YN7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Influenza A virus (strain A/Swine/Iowa/15/1930 H1N1)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-24 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.265 (Depositor) 
• R-Value Work: 
  0.217 (Depositor) 

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 
• DOI: https://doi.org/10.1038/ni0405-365
• Primary Citation Related Structures: 
  1YN6, 1YN7

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.74 kDa 
• Atom Count: 3,378 
• Modeled Residue Count: 383 
• Deposited Residue Count: 383 
• Unique protein chains: 3

Macromolecules

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 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 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): 1  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.265 (Depositor) 
• R-Value Work:  0.217 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.306	α = 90
b = 56.306	β = 90
c = 274.272	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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: 2021-11-10
  Changes: Database references
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary