Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 44782.24 
• Atom Count: 3155 
• Residue Count: 383 
• Unique protein chains: 3

1INQ

Structure of Minor Histocompatibility Antigen peptide, H13a, complexed to H2-Db

• DOI: 10.2210/pdb1INQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli


• Deposited: 2001-05-14 Released: 2002-03-20 
• Deposition Author(s): Ostrov, D.A., Roden, M.M., Shi, W., Palmieri, E., Christianson, G.J., Mendoza, L., Villaflor, G., Tilley, D., Shastri, N., Grey, H., Almo, S.C., Roopenian, D., Nathenson, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 

Literature

How H13 histocompatibility peptides differing by a single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself discrimination.

Ostrov, D.A., Roden, M.M., Shi, W., Palmieri, E., Christianson, G.J., Mendoza, L., Villaflor, G., Tilley, D., Shastri, N., Grey, H., Almo, S.C., Roopenian, D., Nathenson, S.G.

(2002) J.Immunol. 168: 283-289

• PubMed: 11751972 
• DOI: 10.4049/jimmunol.168.1.283
• Primary Citation of Related Structures:  
  1JUF


• PubMed Abstract: 
  

The mouse H13 minor histocompatibility (H) Ag, originally detected as a barrier to allograft transplants, is remarkable in that rejection is a consequence of an extremely subtle interchange, P4(Val/Ile), in a nonamer H2-D(b)-bound peptide. Moreover, H13 peptides lack the canonical P5(Asn) central anchor residue normally considered important for forming a peptide/MHC complex. To understand how these noncanonical peptide pMHC complexes form physiologically active TCR ligands, crystal structures of allelic H13 pD(b) complexes and a P5(Asn) anchored pD(b) analog were solved to high resolution. The structures show that the basis of TCRs to distinguish self from nonself H13 peptides is their ability to distinguish a single solvent-exposed methyl group. In addition, the structures demonstrate that there is no need for H13 peptides to derive any stabilization from interactions within the central C pocket to generate fully functional pMHC complexes. These results provide a structural explanation for a classical non-MHC-encoded H Ag, and they call into question the requirement for contact between anchor residues and the major MHC binding pockets in vaccine design.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, 1600 Morris Boulevard, Bronx, NY 10461, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN	A	275	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
Find proteins for P01899 (Mus musculus) Go to UniProtKB:  P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
BETA-2 MICROGLOBULIN	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB:  P01887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MHC Class I H13a minor histocompatibility peptide	C	9	Mus musculus	Mutation(s): 0  Gene Names: Hm13 (H13, Psl3) EC: 3.4.23.-
Find proteins for Q9D8V0 (Mus musculus) Go to UniProtKB:  Q9D8V0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 92.640	α = 90.00
b = 109.420	β = 120.01
c = 57.560	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-14 
• Released Date: 2002-03-20 
• Deposition Author(s): Ostrov, D.A., Roden, M.M., Shi, W., Palmieri, E., Christianson, G.J., Mendoza, L., Villaflor, G., Tilley, D., Shastri, N., Grey, H., Almo, S.C., Roopenian, D., Nathenson, S.G.

Revision History 

• Version 1.0: 2002-03-20
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance