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1YDP

HLA-G*01:01 binding "RIIPRHLQL" at 1.90Å 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
HLA-G*01:01
['A']
3. Peptide
RIIPRHLQL
['P']

Species


Locus / Allele group


Publication

Crystal structure of HLA-G: a nonclassical MHC class I molecule expressed at the fetal-maternal interface.

Clements CS, Kjer-Nielsen L, Kostenko L, Hoare HL, Dunstone MA, Moses E, Freed K, Brooks AG, Rossjohn J, McCluskey J
Proc. Natl. Acad. Sci. U.S.A. (2005) 102, 3360-5 [doi:10.1073/pnas.0409676102]  [pubmed:15718280

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

Deposited: 2004-12-25
Released: 2005-03-08
Revised: 2021-11-10

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Nonamer (9 amino acids)

Sequence: RIIPRHLQL

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 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

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

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

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
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

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Complete structures

Aligned structures [cif]
  1. 1YDP assembly 1  

Components

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

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1ydp

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