1MWA

2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.284 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.

Luz, J.G.Huang, M.D.Garcia, K.C.Rudolph, M.G.Teyton, L.Wilson, I.A.

(2002) J.EXP.MED. 195: 1175-1186

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of the 2C/H-2K(bm3)-dEV8 allogeneic complex at 2.4 A and H-2K(bm3)-dEV8 at 2.15 A, when compared with their syngeneic counterparts, elucidate structural changes that induce an alloresponse. The Asp77Ser mutation that imbues H-2 ...

    The crystal structures of the 2C/H-2K(bm3)-dEV8 allogeneic complex at 2.4 A and H-2K(bm3)-dEV8 at 2.15 A, when compared with their syngeneic counterparts, elucidate structural changes that induce an alloresponse. The Asp77Ser mutation that imbues H-2K(bm3)-dEV8 with its alloreactive properties is located beneath the peptide and does not directly contact the T cell receptor (TCR). However, the buried mutation induces local rearrangement of the peptide itself to preserve hydrogen bonding interactions between the peptide and the alpha(1) 77 residue. The COOH terminus of the peptide main chain is tugged toward the alpha(1)-helix such that its presentation to the TCR is altered. These changes increase the stability of the allogeneic peptide-major histocompatibility complex (pMHC) complex and increase complementarity in the TCR-pMHC interface, placing greater emphasis on recognition of the pMHC by the TCR beta-chain, evinced by an increase in shape complementarity, buried surface area, and number of TCR-pMHC contacting residues. A nearly fourfold increase in the number of beta-chain-pMHC contacts is accompanied by a concomitant 64% increase in beta-chain-pMHC shape complementarity. Thus, the allogeneic mutation causes the same peptide to be presented differently, temporally and spatially, by the allogeneic and syngeneic MHCs.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2C T CELL RECEPTOR ALPHA CHAIN
A, C
202Mus musculusMutation(s): 0 
Find proteins for P01738 (Mus musculus)
Go to UniProtKB:  P01738
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2C T CELL RECEPTOR BETA CHAIN
B, D
237Mus musculusMutation(s): 0 
Find proteins for P01851 (Mus musculus)
Go to UniProtKB:  P01851
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
H, I
275Mus musculusMutation(s): 0 
Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MICROGLOBULIN MHC LIGHT CHAIN
L, M
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DEV8
P, Q
8Mus musculusMutation(s): 0 
Gene Names: Ndufa4
Find proteins for Q62425 (Mus musculus)
Go to UniProtKB:  Q62425
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, I, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
P
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.284 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 297.899α = 90.00
b = 95.942β = 90.00
c = 84.735γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance