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5J6H

H2-Q10 binding "VGITNVDL" at 2.30Å 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 with peptide

1. Beta 2 microglobulin
['B']
2. Class I alpha
H2-Q10
['A']
3. Peptide
VGITNVDL
['F']

Species


Locus / Allele group


Publication

Recognition of the MHC class Ib molecule H2-Q10 by the natural killer cell receptor Ly49C.

Sullivan LC, Berry R, Sosnin N, Widjaja JM, Deuss FA, Balaji GR, LaGruta NL, Mirams M, Trapani JA, Rossjohn J, Brooks AG, Andrews DM
J. Biol. Chem. (2016) [doi:10.1074/jbc.m116.737130]  [pubmed:27385590

Murine natural killer (NK) cells are regulated by the interaction of Ly49 receptors with major histocompatibility complex class I molecules (MHC-I). Although the ligands for inhibitory Ly49 were considered to be restricted to classical MHC (MHC-Ia), we have shown that the non-classical MHC molecule (MHC-Ib) H2-M3 was a ligand for the inhibitory Ly49A. Here we establish that another MHC-Ib, H2-Q10, is a bona fide ligand for the inhibitory Ly49C receptor. H2-Q10 bound to Ly49C with a marginally lower affinity (∼5 μm) than that observed between Ly49C and MHC-Ia (H-2K(b)/H-2D(d), both ∼1 μm), and this recognition could be prevented by cis interactions with H-2K in situ To understand the molecular details underpinning Ly49·MHC-Ib recognition, we determined the crystal structures of H2-Q10 and Ly49C bound H2-Q10. Unliganded H2-Q10 adopted a classical MHC-I fold and possessed a peptide-binding groove that exhibited features similar to those found in MHC-Ia, explaining the diverse peptide binding repertoire of H2-Q10. Ly49C bound to H2-Q10 underneath the peptide binding platform to a region that encompassed residues from the α1, α2, and α3 domains, as well as the associated β2-microglobulin subunit. This docking mode was conserved with that previously observed for Ly49C·H-2K(b) Indeed, structure-guided mutation of Ly49C indicated that Ly49C·H2-Q10 and Ly49C·H-2K(b) possess similar energetic footprints focused around residues located within the Ly49C β4-stand and L5 loop, which contact the underside of the peptide-binding platform floor. Our data provide a structural basis for Ly49·MHC-Ib recognition and demonstrate that MHC-Ib represent an extended family of ligands for Ly49 molecules.

Structure deposition and release

Deposited: 2016-04-05
Released: 2016-07-13
Revised: 2020-01-08

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Octamer (8 amino acids)

Sequence: VGITNVDL

Interactive view
Cutaway side view (static)
Surface top view (static - coloured by atom property)
Cutaway top view (static)

Data provenance

MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.


Peptide neighbours

P1 VAL

GLU163
ARG62
ARG66
TRP167
TYR59
GLU63
MET5
TYR7
TYR171
TYR159
P2 GLY

TYR7
TYR159
ARG66
TYR99
GLU63
P3 ILE

GLU9
TYR155
LEU114
TYR156
TRP97
ASN70
TYR99
TYR159
GLU163
ARG66
P4 THR

TYR156
TYR155
ARG66
TRP97
ASN70
P5 ASN

TYR116
SER77
TYR156
ASN70
PHE74
SER73
TRP97
P6 VAL

TYR156
ALA152
TRP147
SER73
TYR116
TYR155
P7 ASP

LYS146
SER77
VAL76
SER73
TRP147
P8 LEU

THR143
ILE95
THR80
TYR123
TYR84
LEU81
PHE74
TRP147
TYR116
LYS146
SER77

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

Data provenance

Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.

Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]


Binding cleft pockets


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

ALA159
ALA163
GLU167
ARG171
SER5
GLU59
ARG63
GLN66
ARG7
B Pocket

ILE24
PHE34
ARG45
ARG63
GLN66
ARG67
ARG7
GLY70
PHE9
MET99
C Pocket

GLY70
GLN73
SER74
PHE9
GLN97
D Pocket

TYR114
GLU155
TYR156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
TYR156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
LYS147
VAL77
ARG80
THR81
GLY84
THR95

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
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

2. Class I alpha
H2-Q10
        10        20        30        40        50        60
MGSHSMRYFETSVSRPGLGEPRFIIVGYVDDTQFVRFDSDAETPRMEPRAPWMEQEGPEY
        70        80        90       100       110       120
WERETQRAKGNEQSFHVSLRTLLGYYNQSESGSHTIQWMYGCKVGSDGRFLRGYLQYAYD
       130       140       150       160       170       180
GRDYIALNEDLKTWTAADVAAIITRRKWEQAGAAEYYRAYLEAECVEWLLRYLELGKETL
       190       200       210       220       230       240
LRTDPPKTHVTHHPGSEGDVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
       250       260       270       280       290       300
TFQKWASVVVPLGKEQNYTCHVYHEGLPEPLTLRWEPPPSTDSIMSHIADLLWPSLKLWW

YL

3. Peptide
VGITNVDL


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. 5J6H assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5J6H assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5J6H assembly 1  
Peptide only [cif]
  1. 5J6H assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5j6h

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