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6AEE

HLA-G*01:01 binding "RIIPRHLQL" with LIRB-1 NK receptor at 3.30Å 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 and lirb1

1. Beta 2 microglobulin
['B', 'E']
2. Class I alpha
HLA-G*01:01
['A', 'D']
3. lirb1
['G', 'H']
4. Peptide
RIIPRHLQL
['C', 'F']

Species


Locus / Allele group


Publication

Structures of the four��Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex.

Wang Q, Song H, Cheng H, Qi J, Nam G, Tan S, Wang J, Fang M, Shi Y, Tian Z, Cao X, An Z, Yan J, Gao GF
Cell. Mol. Immunol. (2019) [doi:10.1038/s41423-019-0258-5]  [pubmed:31273318

Leukocyte immunoglobulin (Ig)-like receptors (LILRs), also known as CD85 and immunoglobulin-like transcripts (ILTs), play pivotal roles in regulating immune responses. These receptors define an immune checkpoint that immune therapy can target. Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Although the discrete domains of LILRB1/2 are clear, the assembly mode of the four extracellular Ig-like domains (D1, D2, D3, and D4) remains unknown. Previous data indicate that D1D2 is responsible for binding to HLA class I (HLA-I), but the roles of D3D4 are still unclear. Here, we determined the crystal structure of the four Ig-like domain LILRB2 and four-domain LILRB1 in complex with HLA-G1. The angles between adjacent domains and the staggered assembly of the four domains suggest limited flexibility and limited plasticity of the receptors during ligand binding. The complex structure of four-domain LILRB1 and HLA-G1 supports the model that D1D2 is responsible for HLA-I binding, while D3D4 acts as a scaffold. Accordingly, cis and trans binding models for HLA-I binding to LILRB1/2 are proposed. The geometries of LILRB1/2 in complex with dimeric and monomeric HLA-G1 suggest the accessibility of the dimeric receptor, which in turn, transduces more inhibitory signals. The assembly of LILRB1/2 and its binding to HLA-G1 could aid in the design of immune regulators and benefit immune interference.

Structure deposition and release

Deposited: 2018-08-04
Released: 2019-07-31
Revised: 2019-07-31

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

PHE33
TYR159
TYR7
THR163
GLU63
MET5
TYR171
TRP167
TYR59
GLU62
P2 ILE

TRP97
THR67
MET45
TYR159
TYR7
HIS70
ALA24
GLU63
ASN66
P3 ILE

HIS70
ARG156
ASN66
GLU114
GLN155
ILE99
TYR159
TRP97
P4 PRO

ASN66
TYR159
ALA69
HIS70
P5 ARG

HIS70
ARG156
GLN155
P6 HIS

THR73
SER9
ASP74
ALA69
TRP97
TYR116
HIS70
ASN77
ARG156
PHE22
P7 LEU

THR73
TRP133
LEU124
ASN77
TYR116
CYS147
ARG156
GLU114
VAL152
ASP74
P8 GLN

THR73
ASN77
MET76
LYS146
P9 LEU

LEU95
TYR123
LEU124
THR80
LEU81
ASN77
TYR84
SER143
TYR116
LYS146

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
GLY163
GLU167
ARG171
SER5
GLU59
GLU63
ARG66
ARG7
B Pocket

ILE24
PHE34
ARG45
GLU63
ARG66
ASN67
ARG7
ALA70
PHE9
MET99
C Pocket

ALA70
GLN73
THR74
PHE9
GLN97
D Pocket

TYR114
GLU155
GLN156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
ASN152
GLN156
GLN97
F Pocket

ARG116
ASP123
ILE143
ARG146
LYS147
MET77
GLN80
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
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
MGSHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEY
        70        80        90       100       110       120
WEEETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLIRGYERYAYD
       130       140       150       160       170       180
GKDYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEML
       190       200       210       220       230       240
QRADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDG
       250       260       270
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRWKQ

3. lirb1
lirb1
        10        20        30        40        50        60
HLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQFP
        70        80        90       100       110       120
IPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTLQ
       130       140       150       160       170       180
CDSQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNS
       190       200       210       220       230       240
PYEWSLPSDLLELLVLGVSKKPSLSVQPGPIVAPEETLTLQCGSDAGYNRFVLYKDGERD
       250       260       270       280       290       300
FLQLAGAQPQAGLSQANFTLGPVSRSYGGQYRCYGAHNLSSEWSAPSDPLDILIAGQFYD
       310       320       330       340       350       360
RVSLSVQPGPTVASGENVTLLCQSQGWMQTFLLTKEGAADDPWRLRSTYQSQKYQAEFPM
       370       380       390
GPVTSAHAGTYRCYGSQSSKPYLLTHPSDPLELHHHHHH

4. 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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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. 6AEE assembly 1  
  2. 6AEE assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 6AEE assembly 1  
  2. 6AEE assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6AEE assembly 1  
  2. 6AEE assembly 2  
Peptide only [cif]
  1. 6AEE assembly 1  
  2. 6AEE assembly 2  

Derived data

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

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