H2-Dd binding "RGPGRAFVTI" with CD8 dimer at 2.60Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Class i with peptide and cd8 dimer
H2-Dd
RGPGRAFVTI
Species
Locus / Allele group
Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position.
In the immune system, B cells, dendritic cells, NK cells, and T lymphocytes all respond to signals received via ligand binding to receptors and coreceptors. Although the specificity of T cell recognition is determined by the interaction of T cell receptors with MHC/peptide complexes, the development of T cells in the thymus and their sensitivity to Ag are also dependent on coreceptor molecules CD8 (for MHC class I (MHCI)) and CD4 (for MHCII). The CD8alphabeta heterodimer is a potent coreceptor for T cell activation, but efforts to understand its function fully have been hampered by ignorance of the structural details of its interactions with MHCI. In this study we describe the structure of CD8alphabeta in complex with the murine MHCI molecule H-2D(d) at 2.6 A resolution. The focus of the CD8alphabeta interaction is the acidic loop (residues 222-228) of the alpha3 domain of H-2D(d). The beta subunit occupies a T cell membrane proximal position, defining the relative positions of the CD8alpha and CD8beta subunits. Unlike the CD8alphaalpha homodimer, CD8alphabeta does not contact the MHCI alpha(2)- or beta(2)-microglobulin domains. Movements of the CD8alpha CDR2 and CD8beta CDR1 and CDR2 loops as well as the flexibility of the H-2D(d) CD loop facilitate the monovalent interaction. The structure resolves inconclusive data on the topology of the CD8alphabeta/MHCI interaction, indicates that CD8beta is crucial in orienting the CD8alphabeta heterodimer, provides a framework for understanding the mechanistic role of CD8alphabeta in lymphoid cell signaling, and offers a tangible context for design of structurally altered coreceptors for tumor and viral immunotherapy.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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
GLU58
TYR59
ARG62
TYR159
TYR7
ARG66
GLU163
GLU63
TRP167
LEU5
TYR171
|
P10
ILE
LYS146
ALA81
ILE142
ASP77
THR80
TYR84
TRP147
THR143
LEU95
TYR123
|
P2
GLY
GLU163
GLU63
TYR7
ARG66
TYR159
|
P3
PRO
TYR159
TRP97
TYR7
TRP114
ARG66
ASN70
ALA99
|
P4
GLY
ASP156
TRP114
ARG66
ASN70
TRP97
|
P5
ARG
TRP97
ARG155
PHE116
TRP114
ASP77
PHE74
TRP147
SER73
ASN70
|
P6
ALA
ASN70
ARG155
|
P7
PHE
GLY69
SER73
GLN72
|
P8
VAL
ALA152
TRP147
SER73
ALA150
ARG155
|
P9
THR
TRP147
SER73
VAL76
ASP77
THR80
THR143
|
Colour key
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]
A Pocket
TYR159
GLU163
TRP167
TYR171
LEU5
TYR59
GLU63
ARG66
TYR7
|
B Pocket
GLU24
VAL34
TYR45
GLU63
ARG66
ALA67
TYR7
ASN70
VAL9
ALA99
|
C Pocket
ASN70
SER73
PHE74
VAL9
TRP97
|
D Pocket
TRP114
ARG155
ASP156
TYR159
LEU160
ALA99
|
E Pocket
TRP114
TRP147
ALA152
ASP156
TRP97
|
F Pocket
PHE116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
TYR84
LEU95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD 70 80 90 WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM |
2. cd8a
cd8a
|
10 20 30 40 50 60
GSGEAKPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVY 70 80 90 100 110 120 MASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSV 130 140 150 160 VPVLQKVNSTTTKPVLRTPSPVHPTGTSQPQRPEDCRPRGSVKGTG |
3. cd8b
cd8b
|
10 20 30 40 50 60
SSALIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGV 70 80 90 100 110 120 LYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDV 130 140 LPTTAPTKKTTLKMKKKKQCPFPHPETQKG |
4. Class I alpha
H2-Dd
|
10 20 30 40 50 60
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW 70 80 90 100 110 120 ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG 130 140 150 160 170 180 CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL 190 200 210 220 230 240 RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWG |
5. Peptide
|
RGPGRAFVTI
|
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
Components
Data license
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.