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6IWH

Mamu-B*051:04 possibly without "peptide" at 1.95Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Class i possibly without peptide

1. Beta 2 microglobulin
['B']
2. Class I alpha
Mamu-B*051:04
['A']

Species


Locus / Allele group


Publication

Identification and Structure of an MHC Class I-Encoded Protein with the Potential to Present N-Myristoylated 4-mer Peptides to T Cells.

Yamamoto Y, Morita D, Shima Y, Midorikawa A, Mizutani T, Suzuki J, Mori N, Shiina T, Inoko H, Tanaka Y, Mikami B, Sugita M
J. Immunol. (2019) 202, 3349-3358 [doi:10.4049/jimmunol.1900087]  [pubmed:31043477

Similar to host proteins, N-myristoylation occurs for viral proteins to dictate their pathological function. However, this lipid-modifying reaction creates a novel class of "lipopeptide" Ags targeted by host CTLs. The primate MHC class I-encoded protein, Mamu-B*098, was previously shown to bind N-myristoylated 5-mer peptides. Nevertheless, T cells exist that recognize even shorter lipopeptides, and much remains to be elucidated concerning the molecular mechanisms of lipopeptide presentation. We, in this study, demonstrate that the MHC class I allele, Mamu-B*05104, binds the N-myristoylated 4-mer peptide (C14-Gly-Gly-Ala-Ile) derived from the viral Nef protein for its presentation to CTLs. A phylogenetic tree analysis indicates that these classical MHC class I alleles are not closely associated; however, the high-resolution x-ray crystallographic analyses indicate that both molecules share lipid-binding structures defined by the exceptionally large, hydrophobic B pocket to accommodate the acylated glycine (G1) as an anchor. The C-terminal isoleucine (I4) of C14-Gly-Gly-Ala-Ile anchors at the F pocket, which is distinct from that of Mamu-B*098 and is virtually identical to that of the peptide-presenting MHC class I molecule, HLA-B51. The two central amino acid residues (G2 and A3) are only exposed externally for recognition by T cells, and the methyl side chain on A3 constitutes a major T cell epitope, underscoring that the epitopic diversity is highly limited for lipopeptides as compared with that for MHC class I-presented long peptides. These structural features suggest that lipopeptide-presenting MHC class I alleles comprise a distinct MHC class I subset that mediates an alternative pathway for CTL activation.

Structure deposition and release

Deposited: 2018-12-05
Released: 2019-08-14
Revised: 2019-08-14

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

TYR159
PRO163
TRP167
TYR171
LEU5
TYR59
GLU63
ARG66
TYR7
B Pocket

TYR24
VAL34
THR45
GLU63
ARG66
ALA67
TYR7
ARG70
GLY9
ALA99
C Pocket

ARG70
THR73
ASP74
GLY9
TRP97
D Pocket

HIS114
ARG155
PHE156
TYR159
LEU160
ALA99
E Pocket

HIS114
TRP147
TYR152
PHE156
TRP97
F Pocket

SER116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
LEU95

Colour key

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

2. Class I alpha
Mamu-B*051:04
        10        20        30        40        50        60
GSHSLRYFGTAVSRPGRGEPRFIYVGYVDDTQFVRFDSDAASPRTEPRAPWVEQEGPEYW
        70        80        90       100       110       120
EEETRRAKARAQTDRADLRTLRGYYNQSEAGSHTLQWMAGCDLGPNGRLLRGYHQSAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWIAADMAAQNTQRKWEATRYAERFRAYLEGPCLEWLRRYLENGKETLQ
       190       200       210       220       230       240
HADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDIEFVETRPAGDGT
       250       260       270
FQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP


Data provenance

Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.


Downloadable data

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Complete structures

Aligned structures [cif]
  1. 6IWH assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6IWH assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6IWH assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6iwh

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes