5XS3

HLA-C*06:02 binding "VRSRRCLRL" at 2.50Å 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.

Complex type

Class i with peptide

1. Beta 2 microglobulin

['B']

2. Class I alpha
HLA-C*06:02

['A']

3. Peptide
VRSRRCLRL

['C']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-C / HLA-C*06

Publication

Characterization of Autoantigen Presentation by HLA-C*06:02 in Psoriasis.

Wei P, Yang Y, Liu Z, Luo Z, Tu W, Han J, Deng Y, Yin L

J. Invest. Dermatol. (2017) [doi:10.1016/j.jid.2017.05.036] [pubmed:28655516]

Structure deposition and release

Deposited: 2017-06-12

Released: 2017-09-13

Revised: 2017-10-11

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: VRSRRCLRL

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

TRP167

MET5

TYR159

LYS66

GLU63

TYR59

TYR7

TYR99

TYR171

PHE33

P2 ARG

TYR99

SER24

TRP97

PHE8

TYR67

PHE22

TYR159

ASP9

LYS66

GLU63

GLN70

TYR7

P3 SER

TYR159

LYS66

TYR99

TRP156

P4 ARG

ARG62

LYS66

GLU63

P5 ARG

GLU152

TRP97

TRP156

GLN155

GLN70

P6 CYS

ARG69

TRP97

GLN70

ALA73

LYS66

GLU152

P7 LEU

TRP97

ASP74

SER116

GLN70

ALA73

ASN77

TRP147

LEU95

ASP114

P8 ARG

ALA73

LYS80

THR143

ASN77

TRP147

P9 LEU

LEU81

LYS146

ILE142

TYR84

TYR123

LYS80

THR143

ASN77

TRP147

LEU95

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

TYR66

PHE7

B Pocket

VAL24

ARG34

GLU45

THR63

TYR66

LYS67

PHE7

ALA70

THR9

GLY99

C Pocket

ALA70

ASP73

ARG74

THR9

MET97

D Pocket

GLN114

TRP155

ARG156

LEU159

GLU160

GLY99

E Pocket

GLN114

GLU147

ALA152

ARG156

MET97

F Pocket

ALA116

ILE123

GLN143

TRP146

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 MQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSGDW 70 80 90 SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

2. Class I alpha HLA-C06:02 IPD-IMGT/HLA* [ipd-imgt:HLA35196]	10 20 30 40 50 60 SHSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWD 70 80 90 100 110 120 RETQKYKRQAQADRVNLRKLRGYYNQSEDGSHTLQWMYGCDLGPDGRLLRGYDQSAYDGK 130 140 150 160 170 180 DYIALNEDLRSWTAADTAAQITQRKWEAAREAEQWRAYLEGTCVEWLRRYLENGKETLQR 190 200 210 220 230 240 AEHPKTHVTHHPVSDHEATLRCWALGFYPARITLTWQRDGEDQTQDTELVETRPAGDGTF 250 260 270 QKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW

3. Peptide	VRSRRCLRL

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.

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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]

5XS3 assembly 1

Components

MHC Class I alpha chain [cif]

5XS3 assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

5XS3 assembly 1

Peptide only [cif]

5XS3 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/5xs3

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

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.