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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Ligand Structure Quality Assessment 


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: 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) ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
2C T CELL RECEPTOR ALPHA CHAINA,
B [auth C]
202Mus musculusMutation(s): 0 
UniProt
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UniProt GroupP01738
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2C T CELL RECEPTOR BETA CHAINC [auth B],
D
237Mus musculusMutation(s): 0 
UniProt
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UniProt GroupP01851
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAINE [auth H],
F [auth I]
275Mus musculusMutation(s): 0 
Gene Names: H2-K1H2-K
UniProt
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UniProt GroupP01901
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MICROGLOBULIN MHC LIGHT CHAING [auth L],
H [auth M]
99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DEV8I [auth P],
J [auth Q]
8N/AMutation(s): 0 
UniProt
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UniProt GroupQ62425
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Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth E],
O [auth K]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
Q [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

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P [auth A],
R [auth I],
S [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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T [auth P]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
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