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3DMM

H2-Dd binding "RGPGRAFVTI" with CD8 dimer at 2.60Å 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 cd8 dimer

1. Beta 2 microglobulin
['B']
2. cd8a
['C']
3. cd8b
['D']
4. Class I alpha
H2-Dd
['A']
5. Peptide
RGPGRAFVTI
['P']

Species


Locus / Allele group


Publication

Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position.

Wang R, Natarajan K, Margulies DH
J. Immunol. (2009) 183, 2554-64 [doi:10.4049/jimmunol.0901276]  [pubmed:19625641

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

Deposited: 2008-07-01
Released: 2009-07-14
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: Decamer (10 amino acids)

Sequence: RGPGRAFVTI

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

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

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]


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
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

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

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

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Complete structures

Aligned structures [cif]
  1. 3DMM assembly 1  

Components

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

Derived data

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

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