Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 141185.08 
• Atom Count: 9908 
• Residue Count: 1200 
• Unique protein chains: 4

1R5I

Crystal structure of the MAM-MHC complex

• DOI: 10.2210/pdb1R5I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mycoplasma arthritidis, Influenza A virus (strain A/Swine/Hong Kong/81/1978 H3N2)
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)


• Deposited: 2003-10-10 Released: 2004-03-16 
• Deposition Author(s): Zhao, Y., Li, Z., Drozd, S.J., Guo, Y., Mourad, W., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.246 
• R-Value Work: 0.238 

Literature

Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex.

Zhao, Y., Li, Z., Drozd, S.J., Guo, Y., Mourad, W., Li, H.

(2004) Structure 12: 277-288

• PubMed: 14962388 
• DOI: 10.1016/j.str.2004.01.008


• PubMed Abstract: 
  

Mycoplasma arthritidis-derived mitogen (MAM) is a superantigen that can activate large fractions of T cells bearing particular TCR Vbeta elements. Here we report the crystal structure of MAM complexed with a major histocompatibility complex (MHC) antigen, HLA-DR1, loaded with haemagglutinin peptide 306-318 (HA). The structure reveals that MAM has a novel fold composed of two alpha-helical domains. This fold is entirely different from that of the pyrogenic superantigens, consisting of a beta-grasped motif and a beta barrel. In the complex, the N-terminal domain of MAM binds orthogonally to the MHC alpha1 domain and the bound HA peptide, and to a lesser extent to the MHC beta1 domain. Two MAM molecules form an asymmetric dimer and cross-link two MHC antigens to form a plausible, dimerized MAM-MHC complex. These data provide the first crystallographic evidence that superantigens can dimerize MHC molecules. Based on our structure, a model of the TCR2MAM2MHC2 complex is proposed.

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Organizational Affiliation: 

Wadsworth Center, New York State Department of Health, Empire State Plaza, PO Box 509, Albany, NY 12201, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A, E	181	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens) Go to Gene View: HLA-DRA Go to UniProtKB:  P01903

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, F	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P04229 (Homo sapiens) Go to Gene View: HLA-DRB1 Go to UniProtKB:  P04229

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin peptide	C, G	13	Influenza A virus (strain A/Swine/Hong Kong/81/1978 H3N2)	Mutation(s): 0  Gene Names: HA
Find proteins for P11133 (Influenza A virus (strain A/Swine/Hong Kong/81/1978 H3N2)) Go to UniProtKB:  P11133

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
superantigen	D, H	216	Mycoplasma arthritidis	Mutation(s): 0
Find proteins for Q48898 (Mycoplasma arthritidis) Go to UniProtKB:  Q48898

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	C, D, E, H	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.246 
• R-Value Work: 0.238 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 138.286	α = 90.00
b = 178.814	β = 90.00
c = 179.554	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SOLVE	phasing
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-10 
• Released Date: 2004-03-16 
• Deposition Author(s): Zhao, Y., Li, Z., Drozd, S.J., Guo, Y., Mourad, W., Li, H.

Revision History 

• Version 1.0: 2004-03-16
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance