1MWA

2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.285 

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This is version 2.0 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

  • DOI: https://doi.org/10.1084/jem.20011644
  • Primary Citation of Related Structures:  
    1LEG, 1LEK, 1MWA

  • 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-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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2C T CELL RECEPTOR ALPHA CHAINA,
B [auth C]
202Mus musculusMutation(s): 0 
UniProt
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Go to UniProtKB:  P01738
Entity Groups  
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UniProt GroupP01738
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01738-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2C T CELL RECEPTOR BETA CHAINC [auth B],
D
237Mus musculusMutation(s): 0 
UniProt
Find proteins for P01851 (Mus musculus)
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Entity Groups  
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UniProt GroupP01851
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P01851-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAINE [auth H],
F [auth I]
275Mus musculusMutation(s): 0 
UniProt
Find proteins for P01901 (Mus musculus)
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UniProt GroupP01901
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01901-1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MICROGLOBULIN MHC LIGHT CHAING [auth L],
H [auth M]
99Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DEV8I [auth P],
J [auth Q]
8N/AMutation(s): 0 
UniProt
Find proteins for Q62425 (Mus musculus)
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Go to UniProtKB:  Q62425
Entity Groups  
UniProt GroupQ62425
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth E],
O [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth F],
M [auth G],
N [auth J]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.285 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 297.899α = 90
b = 95.942β = 90
c = 84.735γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary