HLA-G*01:01 binding "RIIPRHLQL" at 1.90Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
HLA-G*01:01
RIIPRHLQL
Species
Locus / Allele group
Crystal structure of HLA-G: a nonclassical MHC class I molecule expressed at the fetal-maternal interface.
HLA-G is a nonclassical major histocompatibility complex class I (MHC-I) molecule that is primarily expressed at the fetal-maternal interface, where it is thought to play a role in protecting the fetus from the maternal immune response. HLA-G binds a limited repertoire of peptides and interacts with the inhibitory leukocyte Ig-like receptors LIR-1 and LIR-2 and possibly with certain natural killer cell receptors. To gain further insights into HLA-G function, we determined the 1.9-A structure of a monomeric HLA-G complexed to a natural endogenous peptide ligand from histone H2A (RIIPRHLQL). An extensive network of contacts between the peptide and the antigen-binding cleft reveal a constrained mode of binding reminiscent of the nonclassical HLA-E molecule, thereby providing a structural basis for the limited peptide repertoire of HLA-G. The alpha3 domain of HLA-G, a candidate binding site for the LIR-1 and -2 inhibitory receptors, is structurally distinct from the alpha3 domains of classical MHC-I molecules, providing a rationale for the observed affinity differences for these ligands. The structural data suggest a head-to-tail mode of dimerization, mediated by an intermolecular disulfide bond, that is consistent with the observation of HLA-G dimers on the cell surface.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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
ARG
TYR59
GLU62
TYR159
TYR171
GLU58
PHE33
THR163
GLU63
MET5
TRP167
TYR7
|
P2
ILE
GLU63
TYR7
HIS70
TYR159
ASN66
TRP97
MET45
THR67
ALA24
|
P3
ILE
ILE99
HIS70
TYR159
ARG156
ASN66
TRP97
GLN155
|
P4
PRO
ALA69
HIS70
TYR159
ASN66
|
P5
ARG
ARG156
HIS70
GLN155
|
P6
HIS
ARG156
PHE22
THR73
TRP97
HIS70
SER9
ASP74
TYR116
ASN77
|
P7
LEU
ARG156
LEU124
THR73
TRP133
GLU114
TYR116
CYS147
ASN77
VAL152
|
P8
GLN
LYS146
THR73
CYS147
ASN77
|
P9
LEU
TYR123
SER143
LEU95
LYS146
LEU124
TYR84
TYR116
LEU81
ILE142
ASN77
THR80
|
Colour key
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]
A Pocket
LEU159
CYS163
LEU167
LEU171
ARG5
TRP59
THR63
THR66
PHE7
|
B Pocket
MET24
ARG34
GLU45
THR63
THR66
LYS67
PHE7
ALA70
ALA9
GLY99
|
C Pocket
ALA70
ASP73
ARG74
ALA9
MET97
|
D Pocket
ARG114
ARG155
ARG156
LEU159
GLU160
GLY99
|
E Pocket
ARG114
GLU147
ALA152
ARG156
MET97
|
F Pocket
ALA116
LEU123
LYS143
CYS146
GLU147
LEU77
LEU80
ARG81
TYR84
GLN95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
HLA-G*01:01
IPD-IMGT/HLA
[ipd-imgt:HLA34359] |
10 20 30 40 50 60
SHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEYWE 70 80 90 100 110 120 EETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLIRGYERYAYDGK 130 140 150 160 170 180 DYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEMLQR 190 200 210 220 230 240 ADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDGTF 250 260 270 QKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRWKQ |
3. Peptide
|
RIIPRHLQL
|
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
Components
Data license
Footnotes
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
This work is licensed under a Creative Commons Attribution 4.0 International License.