4ZFZ

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex

Morita, D., Yamamoto, Y., Mizutani, T., Ishikawa, T., Suzuki, J., Igarashi, T., Mori, N., Shiina, T., Inoko, H., Fujita, H., Iwai, K., Tanaka, Y., Mikami, B., Sugita, M.

(2016) Nat Commun 7: 10356-10356

  • DOI: 10.1038/ncomms10356
  • Primary Citation of Related Structures:  
    4ZFZ

  • PubMed Abstract: 

    • The covalent conjugation of a 14-carbon saturated fatty acid (myristic acid) to the amino-terminal glycine residue is critical for some viral proteins to function. This protein lipidation modification, termed N-myristoylation, is targeted by host cyt ...

    The covalent conjugation of a 14-carbon saturated fatty acid (myristic acid) to the amino-terminal glycine residue is critical for some viral proteins to function. This protein lipidation modification, termed N-myristoylation, is targeted by host cytotoxic T lymphocytes (CTLs) that specifically recognize N-myristoylated short peptides; however, the molecular mechanisms underlying lipopeptide antigen (Ag) presentation remain elusive. Here we show that a primate major histocompatibility complex (MHC) class I-encoded protein is capable of binding N-myristoylated 5-mer peptides and presenting them to specific CTLs. A high-resolution X-ray crystallographic analysis of the MHC class I:lipopeptide complex reveals an Ag-binding groove that is elaborately constructed to bind N-myristoylated short peptides rather than prototypic 9-mer peptides. The identification of lipopeptide-specific, MHC class I-restricted CTLs indicates that the widely accepted concept of MHC class I-mediated presentation of long peptides to CTLs may need some modifications to incorporate a novel MHC class I function of lipopeptide Ag presentation.

    Organizational Affiliation: 

    Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class IA, D, G, J277Macaca mulattaMutation(s): 0 
Gene Names: Mamu-B, B
Find proteins for K4MU32 (Macaca mulatta)
Explore K4MU32 
Go to UniProtKB:  K4MU32
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E, H, K100Macaca mulattaMutation(s): 0 
Gene Names: B2M
Find proteins for Q6V7J5 (Macaca mulatta)
Explore Q6V7J5 
Go to UniProtKB:  Q6V7J5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5-mer lipopeptide from Protein NefC, F, I, L5Simian immunodeficiency virus (F236/SMH4 ISOLATE) (SOOTY MANGABEY)Mutation(s): 0 
Gene Names: nef
Find proteins for P12482 (Simian immunodeficiency virus (isolate F236/smH4))
Explore P12482 
Go to UniProtKB:  P12482
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR
Download Ideal Coordinates CCD File 
C, F, I, L
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
A, D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B, D, E, G, H, J, K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A, B, D, E, G, H, J, K
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A, G, J
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.402α = 89.2
b = 85.179β = 79.57
c = 127.99γ = 90.02
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-04-22 
  • Released Date: 2016-01-13 
    • Deposition Author(s): Morita, D., Sugita, M.

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations