3BEW

Gaga-BF2*021:01 binding "REVDEQLLSV" at 2.60Å 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', 'E']

2. Class I alpha
Gaga-BF2*021:01

['A', 'D']

3. Peptide
REVDEQLLSV

['C', 'F']

Species

Gallus gallus (Chicken)

Locus / Allele group

GAGA-BF2 / Gaga-BF2*021

Publication

Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding.

Koch M, Camp S, Collen T, Avila D, Salomonsen J, Wallny HJ, van Hateren A, Hunt L, Jacob JP, Johnston F, Marston DA, Shaw I, Dunbar PR, Cerundolo V, Jones EY, Kaufman J

Immunity (2007) 27, 885-99 [doi:10.1016/j.immuni.2007.11.007] [pubmed:18083574]

Little is known about the structure of major histocompatibility complex (MHC) molecules outside of mammals. Only one class I molecule in the chicken MHC is highly expressed, leading to strong genetic associations with infectious pathogens. Here, we report two structures of the MHC class I molecule BF2*2101 from the B21 haplotype, which is known to confer resistance to Marek's disease caused by an oncogenic herpesvirus. The binding groove has an unusually large central cavity, which confers substantial conformational flexibility to the crucial residue Arg9, allowing remodeling of key peptide-binding sites. The coupled variation of anchor residues from the peptide, utilizing a charge-transfer system unprecedented in MHC molecules, allows peptides with conspicuously different sequences to be bound. This promiscuous binding extends our understanding of ways in which MHC class I molecules can present peptides to the immune system and might explain the resistance of the B21 haplotype to Marek's disease.

Structure deposition and release

Deposited: 2007-11-20

Released: 2008-01-01

Revised: 2011-07-13

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Decamer (10 amino acids)

Sequence: REVDEQLLSV

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

TRP164

ARG61

LEU5

TYR168

TYR156

TYR58

GLU62

THR160

TYR7

P10 VAL

THR140

LYS143

TRP95

ASN76

ILE79

PHE120

ARG83

PRO139

LEU80

P2 GLU

MET34

ILE65

GLU62

TYR7

ARG9

VAL66

TYR156

ASP24

P3 VAL

ARG9

LEU153

TYR156

SER97

HIS111

ILE65

P4 ASP

ILE65

P5 GLU

ILE72

GLN64

ILE65

SER69

GLY68

P6 GLN

TYR149

ILE72

P7 LEU

TRP144

GLY152

LEU153

TRP95

HIS111

TYR149

P8 LEU

ASN73

ARG9

TRP95

ASN76

SER69

SER97

ILE72

HIS111

P9 SER

TYR149

TRP144

THR140

LYS143

TRP95

ASN76

ILE72

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]

Chain sequences

1. Beta 2 microglobulin Beta 2 microglobulin	10 20 30 40 50 60 MDLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDW 70 80 90 TFQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF

2. Class I alpha Gaga-BF2021:01 IPD-MHC* [ipd-mhc:CHICKEN08580]	10 20 30 40 50 60 ELHTLRYIRTAMTDPGPGLPWFVDVGYVDGELFMHYNSTARRAVPRTEWIAANTDQQYWD 70 80 90 100 110 120 RETQIVQGSEQINRENLDILRRRYNQTGGSHTVQWMSGCDILEDGTIRGYHQAAYDGRDF 130 140 150 160 170 180 VAFDKGTMTLTAAVPEAVPTKRKWEEGGYAEGLKQYLEETCVEWLRRYVEYGKAELGRRE 190 200 210 220 230 240 RPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAVRGQDAQSGGIVPNGDGTYHTW 250 260 270 VTIDAQPGDGDKYQCRVEHASLPQPGLYSWR

3. Peptide	REVDEQLLSV

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]

Components

MHC Class I alpha chain [cif]

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

Peptide only [cif]

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/3bew

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.