Alpha This is a work in progress and may change. Your feedback is very welcome.
  


3KYO

HLA-G*01:01 binding "KLPAQFYIL" at 1.70Å 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', 'D']
2. Class I alpha
HLA-G*01:01
['A', 'C']
3. Peptide
KLPAQFYIL
['P', 'Q']

Species


Locus / Allele group


Publication

The structure and stability of the monomorphic HLA-G are influenced by the nature of the bound peptide.

Walpole NG, Kjer-Nielsen L, Kostenko L, McCluskey J, Brooks AG, Rossjohn J, Clements CS
J. Mol. Biol. (2010) 397, 467-80 [doi:10.1016/j.jmb.2010.01.052]  [pubmed:20122941

The highly polymorphic major histocompatibility complex class Ia (MHC-Ia) molecules present a broad array of peptides to the clonotypically diverse alphabeta T-cell receptors. In contrast, MHC-Ib molecules exhibit limited polymorphism and bind a more restricted peptide repertoire, in keeping with their major role in innate immunity. Nevertheless, some MHC-Ib molecules do play a role in adaptive immunity. While human leukocyte antigen E (HLA-E), the MHC-Ib molecule, binds a very restricted repertoire of peptides, the peptide binding preferences of HLA-G, the class Ib molecule, are less stringent, although the basis by which HLA-G can bind various peptides is unclear. To investigate how HLA-G can accommodate different peptides, we compared the structure of HLA-G bound to three naturally abundant self-peptides (RIIPRHLQL, KGPPAALTL and KLPQAFYIL) and their thermal stabilities. The conformation of HLA-G(KGPPAALTL) was very similar to that of the HLA-G(RIIPRHLQL) structure. However, the structure of HLA-G(KLPQAFYIL) not only differed in the conformation of the bound peptide but also caused a small shift in the alpha2 helix of HLA-G. Furthermore, the relative stability of HLA-G was observed to be dependent on the nature of the bound peptide. These peptide-dependent effects on the substructure of the monomorphic HLA-G are likely to impact on its recognition by receptors of both innate and adaptive immune systems.

Structure deposition and release

Deposited: 2009-12-06
Released: 2010-02-23
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: KLPAQFYIL

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 LYS

TYR171
TYR159
TYR59
GLU62
ASN66
GLU63
TYR7
THR163
TRP167
MET5
P2 LEU

ASN66
GLU63
MET45
TYR7
THR163
TRP97
THR67
TYR159
P3 PRO

TYR159
TYR7
ARG156
ASN66
TRP97
ILE99
P4 ALA

ASN66
P5 GLN

ARG156
GLN155
P6 PHE

TRP97
THR73
ALA69
HIS70
ARG156
ASN66
P7 TYR

VAL152
ASN77
ARG156
GLU114
TYR116
GLN155
THR73
ASP74
P8 ILE

THR73
LYS146
ASN77
P9 LEU

ASN77
TYR123
LYS146
TYR84
TYR116
SER143
LEU124
THR80
LEU81
LEU95
ILE142

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
QKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRW

3. Peptide
KLPAQFYIL


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

Data can be downloaded to your local machine from the links below.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
   e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 3KYO assembly 1  
  2. 3KYO assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 3KYO assembly 1  
  2. 3KYO assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3KYO assembly 1  
  2. 3KYO assembly 2  
Peptide only [cif]
  1. 3KYO assembly 1  
  2. 3KYO assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3kyo

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