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3BEV

Gaga-BF2*021:01 binding "GHAEEYGAETL" at 2.10Å 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']
2. Class I alpha
Gaga-BF2*021:01
['A']
3. Peptide
GHAEEYGAETL
['C']

Species

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: 2017-10-25

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Undecamer (11 amino acids)

Sequence: GHAEEYGAETL

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

ARG61
LEU5
TRP164
TYR168
TYR156
GLU62
TYR7
TYR58
 P10 THR

ILE72
TRP95
TYR149
LYS143
ASN76
TRP144
THR140
 P11 LEU

LYS143
ALA113
VAL121
ASN76
LEU80
PRO139
THR140
VAL93
ILE79
ARG83
TRP95
PHE120
 P2 HIS

MET34
TYR7
GLU62
ARG9
VAL66
ASP24
ARG61
ILE65
TRP164
TYR156
 P3 ALA

ILE65
TYR156
 P4 GLU

ARG61
ILE65
 P5 GLU

TYR149
 P6 TYR

GLY68
GLN64
ILE65
ILE72
SER69
 P7 GLY

ILE72
TYR149
TRP144
 P8 ALA

LEU153
TRP95
HIS111
TYR149
TRP144
 P9 GLU

HIS111
TRP144
ASN73
ARG9
ILE72
TRP95
ASN76
SER69

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-BF2*021:01
        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
VTIDAQPGDGDKYQCRVEHASLPQPGLYSWRSGG
3. Peptide
GHAEEYGAETL

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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Complete structures

Aligned structures [cif]
  1. 3BEV assembly 1  

Components

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

Derived data

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

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.