3D2U

Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor

Yang, Z.Bjorkman, P.J.

(2008) Proc Natl Acad Sci U S A 105: 10095-10100

  • DOI: 10.1073/pnas.0804551105
  • Primary Citation of Related Structures:  
    3D2U

  • PubMed Abstract: 
  • UL18 is a human cytomegalovirus class I MHC (MHCI) homolog that binds the host inhibitory receptor LIR-1 and the only known viral MHC homolog that presents peptides. The 2.2-A structure of a LIR-1/UL18/peptide complex reveals increased contacts and o ...

    UL18 is a human cytomegalovirus class I MHC (MHCI) homolog that binds the host inhibitory receptor LIR-1 and the only known viral MHC homolog that presents peptides. The 2.2-A structure of a LIR-1/UL18/peptide complex reveals increased contacts and optimal surface complementarity in the LIR-1/UL18 interface compared with LIR/MHCI interfaces, resulting in a >1,000-fold higher affinity. Despite sharing only approximately 25% sequence identity, UL18's structure and peptide binding are surprisingly similar to host MHCI. The crystal structure suggests that most of the UL18 surface, except where LIR-1 and the host-derived light chain bind, is covered by carbohydrates attached to 13 potential N-glycosylation sites, thereby preventing access to bound peptide and association with most MHCI-binding proteins. The LIR-1/UL18 structure demonstrates how a viral protein evolves from its host ancestor to impede unwanted interactions while preserving and improving its receptor-binding site.


    Organizational Affiliation

    Division of Biology 114-96 and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBF99Homo sapiensMutation(s): 3 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
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PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ActinCG9Homo sapiensMutation(s): 5 
Gene Names: ACTB
Find proteins for P60709 (Homo sapiens)
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PHAROS  P60709
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UL18 proteinAE281Human betaherpesvirus 5Mutation(s): 5 
Find proteins for P08560 (Human cytomegalovirus (strain AD169))
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Go to UniProtKB:  P08560
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Leukocyte immunoglobulin-like receptor subfamily B member 1DH198Homo sapiensMutation(s): 3 
Gene Names: LILRB1ILT2LIR1MIR7
Find proteins for Q8NHL6 (Homo sapiens)
Explore Q8NHL6 
Go to UniProtKB:  Q8NHL6
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PHAROS  Q8NHL6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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A, E
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

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A
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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A
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
FUC
Query on FUC

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A
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.366α = 90
b = 98.11β = 98.46
c = 172.147γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2019-12-25
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary