1MUJ

Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of MHC class II I-Ab in complex with a human CLIP peptide: Prediction of an I-Ab peptide-binding motif

Zhu, Y.Rudensky, A.Y.Teyton, A.L.Wilson, I.A.

(2003) J Mol Biol 326: 1157-1174

  • DOI: 10.1016/s0022-2836(02)01437-7
  • Primary Citation of Related Structures:  
    1MUJ

  • PubMed Abstract: 
  • Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure of the murine class II MHC molecule I-A(b) in complex with human CLIP at 2 ...

    Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure of the murine class II MHC molecule I-A(b) in complex with human CLIP at 2.15A resolution. The structure of I-A(b) accounts, via the peptide-binding groove's unique physicochemistry, for the distinct peptide repertoire bound by this allele. CLIP adopts a similar conformation to peptides bound by other I-A alleles, reinforcing the notion that CLIP is presented as a conventional peptide antigen. When compared to the related HLA-DR3/CLIP complex structure, the CLIP peptide displays a slightly different conformation and distinct interaction pattern with residues in I-A(b). In addition, after examining the published sequences of peptides presented by I-A(b), we discuss the possibility of predicting peptide alignment in the I-A(b) binding groove using a simple scoring matrix.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAINA190Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus)
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Go to UniProtKB:  P14434
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAINB197Mus musculusMutation(s): 0 
Gene Names: H2-Ab1H2-iabeta
UniProt
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CLIP peptideC36Homo sapiensMutation(s): 0 
Gene Names: CD74DHLAG
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens)
Explore P04233 
Go to UniProtKB:  P04233
PHAROS:  P04233
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.647α = 90
b = 88.065β = 92.48
c = 83.74γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2002-09-23 
  • Released Date: 2003-02-18 
  • Deposition Author(s): Zhu, Y., Wilson, I.A.

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-18
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary