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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class IADGJ277Macaca mulattaMutation(s): 0 
Gene Names: Mamu-BB
Find proteins for K4MU32 (Macaca mulatta)
Explore K4MU32 
Go to UniProtKB:  K4MU32
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBEHK100Macaca 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 NefCFIL5Simian 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

View Full Validation Report



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