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3RGV

H2-Kb presenting "WIYVYRPMGCGGS" to Alpha/Beta T cell receptor at 2.90Å 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 alpha beta tcr

1. Beta 2 microglobulin
['D']
2. Class I alpha
H2-Kb
['C']
3. Peptide
WIYVYRPMGCGGS
['E']
4. T cell receptor alpha
TRAV6
['A']
5. T cell receptor beta
TRBV13
['B']

Species


Locus / Allele group


Publication

A single T cell receptor bound to major histocompatibility complex class I and class II glycoproteins reveals switchable TCR conformers.

Yin L, Huseby E, Scott-Browne J, Rubtsova K, Pinilla C, Crawford F, Marrack P, Dai S, Kappler JW
Immunity (2011) 35, 23-33 [doi:10.1016/j.immuni.2011.04.017]  [pubmed:21683626

Major histocompatibility complex class I (MHCI) and MHCII proteins differ in structure and sequence. To understand how T cell receptors (TCRs) can use the same set of variable regions to bind both proteins, we have presented a comparison of a single TCR bound to both MHCI and MHCII ligands. The TCR adopts similar orientations on both ligands with TCR amino acids thought to be evolutionarily conserved for MHC interaction occupying similar positions on the MHCI and MHCII helices. However, the TCR antigen-binding loops use different conformations when interacting with each ligand. Most importantly, we observed alternate TCR core conformations. When bound to MHCI, but not MHCII, Vα disengages from the Jα β strand, switching Vα's position relative to Vβ. In several other structures, either Vα or Vβ undergoes this same modification. Thus, both TCR V-domains can switch among alternate conformations, perhaps extending their ability to react with different MHC-peptide ligands.

Structure deposition and release

Deposited: 2011-04-09
Released: 2011-07-20
Revised: 2011-08-03

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Tridecamer (13 amino acids)

Sequence: WIYVYRPMGCGGS

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 TRP

THR163
GLU63
TRP167
LEU5
TYR159
ARG62
LYS66
TYR171
TYR59
TYR7
P10 CYS

LYS146
LEU81
ALA139
THR143
TYR123
ILE142
THR80
CYS84
P11 GLY

ALA139
MET138
ILE142
CYS84
ALA140
P12 GLY

TYR85
ALA139
MET138
ILE142
CYS84
P13 SER

ASP137
TYR85
ALA139
MET138
CYS84
P2 ILE

TYR159
LYS66
ASN70
VAL9
TYR45
TYR7
GLU24
GLU63
ALA67
P3 TYR

ARG155
ASN70
TYR159
LEU156
LYS66
GLN114
GLU152
P4 VAL

ARG155
ASN70
LYS66
P5 TYR

ARG155
PHE74
TYR116
SER73
VAL97
GLN114
ASN70
VAL9
GLU24
TYR22
TYR7
SER99
P6 ARG

GLU152
TRP147
ALA150
ARG155
TYR116
ASP77
P7 PRO

TRP147
SER73
ASP77
P8 MET

LYS146
PHE74
TYR116
LEU81
ILE95
ASP77
TRP147
THR143
TYR123
P9 GLY

ASP77
THR143
ILE142
THR80
LYS146

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
THR163
TRP167
TYR171
LEU5
TYR59
GLU63
LYS66
TYR7
B Pocket

GLU24
VAL34
TYR45
GLU63
LYS66
ALA67
TYR7
ASN70
VAL9
SER99
C Pocket

ASN70
SER73
PHE74
VAL9
VAL97
D Pocket

GLN114
ARG155
LEU156
TYR159
LEU160
SER99
E Pocket

GLN114
TRP147
GLU152
LEU156
VAL97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
CYS84
ILE95

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
GIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

2. Class I alpha
H2-Kb
        10        20        30        40        50        60
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
        70        80        90       100       110       120
ERETQKAKGNEQSFRVDLRTLLGCYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
       130       140       150       160       170       180
SDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
       190       200       210       220       230       240
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE

3. Peptide
WIYVYRPMGCGGS

4. T cell receptor alpha
T cell receptor alpha
TRAV6
        10        20        30        40        50        60
DSVTQMQGQVTLSENDFLFINCTYSTTGYPTLFWYVQYSGEGPQLLLQVTTANNKGSSRG
        70        80        90       100       110       120
FEATYDKGTTSFHLQKTSVQEIDSAVYYCAANSGTYQRFGTGTKLQVVPNIQNPDPAVYQ
       130       140       150       160       170       180
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
       190
ACANAFNNSIIPEDTFFPSP

5. T cell receptor beta
T cell receptor beta
TRBV13
        10        20        30        40        50        60
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
        70        80        90       100       110       120
GYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPE
       130       140       150       160       170       180
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
       190       200       210       220       230
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW


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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   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. 3RGV assembly 1  

Components

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

Derived data

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

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