Alpha This is a work in progress and may change. Your feedback is very welcome.
  


6LHG

Gaga-BF2*004:01 binding "IDWFDGKE" with CD8a at 2.80Å 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*004:01
['A', 'D']
4. Peptide
IDWFDGKE
['C', 'F']

Species

Locus / Allele group

GAGA-BF2 / Gaga-BF2*004

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: IDWFDGKE

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 ILE

TYR58
THR160
TRP164
GLN62
LEU5
TYR168
TYR156
TYR7
 P2 ASP

PHE97
ILE65
ARG9
TYR156
TYR43
TYR7
THR24
GLN62
ASN69
 P3 TRP

PHE97
ILE65
ARG9
TYR156
ARG152
TRP153
ASN69
 P4 PHE

ILE72
LEU68
ARG152
ILE65
ARG9
TRP153
ASN69
 P5 ASP

ILE72
PHE97
ARG111
ARG9
ARG152
TRP153
ASN69
TRP95
ASN73
 P6 GLY

ARG152
GLU149
TRP153
ASN76
ILE72
TRP144
ARG111
 P7 LYS

TRP144
GLU147
LYS143
ASN76
ILE72
 P8 GLU

PHE120
ILE79
ARG80
ARG83
THR140
LYS143
TRP95
ASN76
TRP144

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
FQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPE
2. cd8a
cd8a
        10        20        30        40        50        60
QGQRNTMEARFLNRNMKHPQEGQPLELECMPFNIDNGVSWIRQDKDGKLHFIVYISPLSR
        70        80        90       100       110
TAFPRNERTSSQFEGSKQGSSFRLVVKNFRAQDQGTYFCIANINQMLYFSSGQPAFF
3. Class I alpha
Gaga-BF2*004:01
        10        20        30        40        50        60
ELHTLRYIRTAMTDPGPGQPWFVTVGYVDGELFVHYNSTARRYVPRTEWIAANTDQQYWD
        70        80        90       100       110       120
GQTQIGQLNEQINRENLGIRQRRYNQTGGSHTVQWMFGCDILEDGTIRGYRQSAYDGRDF
       130       140       150       160       170       180
IALDKDMKTFTAAVPEAVPTKRKWEEESEPERWKNYLEETCVEWLRRYVEYGKAELGRRE
       190       200       210       220       230       240
RPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAVRGQDAHSGGIVPNGDGTYHTW
       250       260       270
VTIEAQPGDGDKYQCRVEHASLPQPGLYSWKL
4. Peptide
IDWFDGKE

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]
  1. 6LHG assembly 1  
  2. 6LHG assembly 2  

Components

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

Derived data

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

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.