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6LHF

Gaga-BF2*015:01 binding "RRREQTDY" with CD8a at 2.70Å 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 cd8a

1. Beta 2 microglobulin
['B', 'E']
2. cd8a
['G', 'H', 'I', 'J']
3. Class I alpha
Gaga-BF2*015:01
['A', 'D']
4. Peptide
RRREQTDY
['C', 'F']

Species

Locus / Allele group

GAGA-BF2 / Gaga-BF2*015

Publication

The Combination of CD8���� and Peptide-MHC-I in a Face-to-Face Mode Promotes Chicken ����T Cells Response.

Liu Y, Chen R, Liang R, Sun B, Wu Y, Zhang L, Kaufman J, Xia C
Front Immunol (2020) 11, 605085 [doi:10.3389/fimmu.2020.605085]  [pubmed:33329601] 

The CD8αα homodimer is crucial to both thymic T cell selection and the antigen recognition of cytotoxic T cells. The CD8-pMHC-I interaction can enhance CTL immunity via stabilizing the TCR-pMHC-I interaction and optimizing the cross-reactivity and Ag sensitivity of CD8+ T cells at various stages of development. To date, only human and mouse CD8-pMHC-I complexes have been determined. Here, we resolved the pBF2*1501 complex and the cCD8αα/pBF2*1501 and cCD8αα/pBF2*0401 complexes in nonmammals for the first time. Remarkably, cCD8αα/pBF2*1501 and the cCD8αα/pBF2*0401 complex both exhibited two binding modes, including an "antibody-like" mode similar to that of the known mammal CD8/pMHC-I complexes and a "face-to-face" mode that has been observed only in chickens to date. Compared to the "antibody-like" mode, the "face-to-face" binding mode changes the binding orientation of the cCD8αα homodimer to pMHC-I, which might facilitate abundant γδT cells to bind diverse peptides presented by limited BF2 alleles in chicken. Moreover, the forces involving in the interaction of cCD8αα/pBF2*1501 and the cCD8αα/pBF2*0401 are different in this two binding model, which might change the strength of the CD8-pMHC-I interaction, amplifying T cell cross-reactivity in chickens. The coreceptor CD8αα of TCR has evolved two peptide-MHC-I binding patterns in chickens, which might enhance the T cell response to major or emerging pathogens, including chicken-derived pathogens that are relevant to human health, such as high-pathogenicity influenza viruses.

Structure deposition and release

Deposited: 2019-12-08
Released: 2020-12-09
Revised: 2021-06-23

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Octamer (8 amino acids)

Sequence: RRREQTDY

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

TYR61
TRP167
GLN60
LEU8
TYR171
TYR10
SER64
TYR100
TYR159
GLU65
 P2 ARG

HIS38
VAL28
SER69
TYR10
ASP27
TYR100
ALA46
THR37
TYR159
GLU65
TRP62
TYR39
GLY29
THR68
 P3 ARG

THR68
SER114
THR72
LEU160
LEU98
LEU156
TYR100
TYR159
TYR152
 P4 GLU

ARG71
TYR152
THR68
 P5 GLN

TYR152
THR72
ASP76
LEU98
TYR100
SER12
ILE75
 P6 THR

TRP147
ILE75
TYR152
 P7 ASP

LYS146
TRP147
ASP78
ILE75
 P8 TYR

ARG86
ILE124
TRP147
GLY79
ASP116
ILE75
LEU83
GLN97
THR82
PHE123
ASP76
LYS146
LEU98
VAL96
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]

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
LTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWTF
        70        80        90
QRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPE
2. cd8a
cd8a
        10        20        30        40        50        60
TMEARFLNRNMKHPQEGQPLELECMPFNIDNGVSWIRQDKDGKLHFIVYISPLSRTAFPR
        70        80        90       100       110
NERTSSQFEGSKQGSSFRLVVKNFRAQDQGTYFCIANINQMLYFSSGQPAFF
3. Class I alpha
Gaga-BF2*015:01
        10        20        30        40        50        60
ELHTLRYISTAMTDPGPGQPWYVDVGYVDGELFTHYNSTARRAVPRTEWIAANTDQQYWD
        70        80        90       100       110       120
SETQTSQRTEQIDRDGLGTLQRRYNQTGGSHTVQLMYGCDILEDGTIRGYSQDAYDGRDF
       130       140       150       160       170       180
IAFDKDTMTFTAAVPEAVPTKRKWEEGDYAEGLKQYLEETCVEWLRRYVEYGKAELGRRE
       190       200       210       220       230       240
RPEVRVWGKEADGILTLSCRAHGFYPRPIAVSWLKDGAVQGQDAQSGGIVPNGDGTYHTW
       250       260
VTIDAQPGDGDKYQCRVEHASLPQPGLYSW
4. Peptide
RRREQTDY

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. 6LHF assembly 1  
  2. 6LHF assembly 2  

Components

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

Derived data

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

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.