4ZFZ | pdb_00004zfz

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 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/ncomms10356
  • Primary Citation 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 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, Institute for Virus Research, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.

Macromolecule Content 

  • Total Structure Weight: 181.77 kDa 
  • Atom Count: 13,805 
  • Modeled Residue Count: 1,528 
  • Deposited Residue Count: 1,528 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major histocompatibility complex class I
A, D, G, J
277Macaca mulattaMutation(s): 0 
UniProt
Find proteins for K4MU32 (Macaca mulatta)
Explore K4MU32 
Go to UniProtKB:  K4MU32
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK4MU32
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E, H, K
100Macaca mulattaMutation(s): 0 
Gene Names: B2M
UniProt
Find proteins for Q6V7J5 (Macaca mulatta)
Explore Q6V7J5 
Go to UniProtKB:  Q6V7J5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6V7J5
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
5-mer lipopeptide from Protein Nef
C, F, I, L
5Simian immunodeficiency virus (F236/SMH4 ISOLATE) (SOOTY MANGABEY)Mutation(s): 0 
UniProt
Find proteins for P12482 (Simian immunodeficiency virus (isolate F236/smH4))
Explore P12482 
Go to UniProtKB:  P12482
Entity Groups
UniProt GroupP12482
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYR

Query on MYR



Download:Ideal Coordinates CCD File
BC [auth I],
GB [auth F],
KA [auth C],
ZC [auth L]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
WA [auth D],
Z [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
CC [auth J]
DC [auth J]
HB [auth G]
BA [auth B],
CA [auth B],
CC [auth J],
DC [auth J],
HB [auth G],
IB [auth G],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
P [auth A],
RC [auth K],
SC [auth K],
VB [auth H],
XA [auth E],
YA [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AB [auth E]
AC [auth H]
BB [auth E]
CB [auth E]
DA [auth B]
AB [auth E],
AC [auth H],
BB [auth E],
CB [auth E],
DA [auth B],
DB [auth E],
EA [auth B],
EB [auth E],
EC [auth J],
FA [auth B],
FB [auth E],
FC [auth J],
GA [auth B],
GC [auth J],
HA [auth B],
HC [auth J],
IA [auth B],
IC [auth J],
JA [auth B],
JB [auth G],
JC [auth J],
KB [auth G],
KC [auth J],
LB [auth G],
LC [auth J],
MB [auth G],
MC [auth J],
NB [auth G],
NC [auth J],
OA [auth D],
OB [auth G],
OC [auth J],
PA [auth D],
PB [auth G],
PC [auth J],
Q [auth A],
QA [auth D],
QB [auth G],
R [auth A],
RA [auth D],
RB [auth G],
S [auth A],
SA [auth D],
SB [auth G],
T [auth A],
TA [auth D],
TB [auth G],
TC [auth K],
U [auth A],
UA [auth D],
UC [auth K],
V [auth A],
VA [auth D],
VC [auth K],
W [auth A],
WB [auth H],
WC [auth K],
X [auth A],
XB [auth H],
XC [auth K],
Y [auth A],
YB [auth H],
YC [auth K],
ZA [auth E],
ZB [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth A],
QC [auth J],
UB [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary