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6LHH

Gaga-BF2*015:01 binding "RRREQTDY" at 2.71Å 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*015:01
['A']
3. Peptide
RRREQTDY
['C']

Species


Locus / Allele group


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

TYR171
THR163
LEU8
TYR61
TYR100
TYR159
GLU65
TYR10
TRP167
P2 ARG

TYR10
THR68
GLU65
VAL47
GLY29
HIS38
ALA46
SER69
TYR39
TRP62
TYR100
VAL28
THR37
TYR159
ASP27
P3 ARG

TYR100
SER114
TYR152
LEU98
THR68
LEU156
TYR159
THR72
P4 GLU

THR68
TYR152
ARG71
P5 GLN

TYR100
ILE75
ASP76
THR72
LEU98
TYR152
P6 THR

TRP147
TYR152
ILE75
P7 ASP

TRP147
ASP78
ILE75
LYS146
P8 TYR

TRP147
GLY79
PRO142
ARG86
VAL96
ASP116
LYS146
ILE75
THR82
PHE123
ASP76
THR143
LEU83
GLN97
LEU98

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
DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWT
        70        80        90
FQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF

2. 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

3. 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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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]
  1. 6LHH assembly 1  

Components

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

Derived data

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

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