6Y26

HLA-B*27:05 binding "GRLNAPIKV" at 1.20Å 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-B*27:05

['A']

3. Peptide
GRLNAPIKV

['C']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-B / HLA-B*27

Publication

A CENTRAL PEPTIDE RESIDUE CAN CONTROL MHC POLYMORPHISM-DEPENDENT ANTIGEN PRESENTATION

Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, A.

Structure deposition and release

Deposited: 2020-02-15

Released: 2020-12-23

Revised: 2020-12-23

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: GRLNAPIKV

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 GLY

TYR159

ARG62

TYR99

TYR59

TYR7

CYS164

ILE52

GLU163

GLU63

PHE33

MET5

TYR171

TRP167

P2 ARG

HIS9

PHE36

VAL34

PHE22

TRP167

ILE66

CYS67

PHE8

ARG62

GLY26

GLU45

TYR99

TYR159

TYR7

ARG35

VAL25

THR24

GLU163

GLU63

P3 LEU

LEU156

GLU163

HIS114

ILE66

GLN155

LEU160

TYR99

TYR159

TYR7

P4 ASN

ILE66

TYR159

ARG62

GLU163

P5 ALA

LEU156

GLN155

P6 PRO

ALA69

THR73

P7 ILE

TRP133

GLN155

THR73

LYS70

ASP77

LEU156

TRP147

HIS114

VAL152

P8 LYS

THR73

GLU76

TRP147

ASP77

LYS146

THR143

P9 VAL

TYR123

LYS146

ASP116

ILE124

LEU81

THR80

TRP147

LEU95

ILE142

TYR84

ASP77

THR143

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

TYR159

GLU163

TRP167

TYR171

MET5

TYR59

GLU63

ILE66

TYR7

B Pocket

THR24

VAL34

GLU45

GLU63

ILE66

CYS67

TYR7

LYS70

HIS9

TYR99

C Pocket

LYS70

THR73

ASP74

HIS9

ASN97

D Pocket

HIS114

GLN155

LEU156

TYR159

LEU160

TYR99

E Pocket

HIS114

TRP147

VAL152

LEU156

ASN97

F Pocket

ASP116

TYR123

THR143

LYS146

TRP147

ASP77

THR80

LEU81

TYR84

LEU95

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-B27:05 IPD-IMGT/HLA* [ipd-imgt:HLA34811]	10 20 30 40 50 60 GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW 70 80 90 100 110 120 DRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG 130 140 150 160 170 180 KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ 190 200 210 220 230 240 RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide	GRLNAPIKV

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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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]

6Y26 assembly 1

Components

MHC Class I alpha chain [cif]

6Y26 assembly 1

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

6Y26 assembly 1

Peptide only [cif]

6Y26 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/6y26

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.