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1KJ2

H2-Kb presenting "KVITFIDL" to Alpha/Beta T cell receptor 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 and alpha beta tcr

1. Beta 2 microglobulin
['L', 'M']
2. Class I alpha
H2-Kb
['H', 'I']
3. Peptide
KVITFIDL
['P', 'Q']
4. T cell receptor alpha
TRAV14
['A']
5. T cell receptor beta
TRBV1
['B']

Species

Locus / Allele group

H2-K / H2-Kb

Publication

A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex.

Reiser JB, Grégoire C, Darnault C, Mosser T, Guimezanes A, Schmitt-Verhulst AM, Fontecilla-Camps JC, Mazza G, Malissen B, Housset D
Immunity (2002) 16, 345-54 [doi:10.1016/s1074-7613(02)00288-1]  [pubmed:11911820] 

The elongated complementary-determining region (CDR) 3beta found in the unliganded KB5-C20 TCR protrudes from the antigen binding site and prevents its docking onto the peptide/MHC (pMHC) surface according to a canonical diagonal orientation. We now present the crystal structure of a complex involving the KB5-C20 TCR and an octapeptide bound to the allogeneic H-2K(b) MHC class I molecule. This structure reveals how a tremendously large CDR3beta conformational change allows the KB5-C20 TCR to adapt to the rather constrained pMHC surface and achieve a diagonal docking mode. This extreme case of induced fit also shows that TCR plasticity is primarily restricted to CDR3 loops and does not propagate away from the antigen binding site.

Structure deposition and release

Deposited: 2001-12-04
Released: 2002-03-27
Revised: 2020-07-29

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: KVITFIDL

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 LYS

TYR171
TYR59
TRP167
THR163
GLU63
LEU5
TYR7
TYR159
LYS66
 P2 VAL

TYR7
ASN70
TYR159
LYS66
VAL9
TYR45
GLU24
GLU63
 P3 ILE

LEU156
SER99
ASN70
TYR159
LYS66
GLN114
ARG155
 P4 THR

ASN70
LYS66
ARG155
 P5 PHE

VAL97
TYR22
SER73
ASN70
PHE74
GLN114
VAL9
ARG155
TYR116
SER99
 P6 ILE

GLU152
ARG155
TRP147
ASP77
TYR116
SER73
 P7 ASP

VAL76
THR143
LYS146
SER73
TRP147
ASP77
 P8 LEU

ILE124
LYS146
TRP147
TYR84
ILE142
ASP77
THR80
TYR116
THR143
LEU81
ILE95
TYR123

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
TYR84
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
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
        70        80        90
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM
2. Class I alpha
H2-Kb
        10        20        30        40        50        60
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
        70        80        90       100       110       120
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
       130       140       150       160       170       180
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
       190       200       210       220       230       240
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPP
3. Peptide
KVITFIDL
4. T cell receptor alpha
T cell receptor alpha
TRAV14
        10        20        30        40        50        60
QQVRQSPQSLTVWEGETAILNCSYEDSTFNYFPWYQQFPGEGPALLISIRSVSDKKEDGR
        70        80        90       100       110
FTIFFNKREKKLSLHITDSQPGDSATYFCAARYQGGRALIFGTGTTVSVSP
5. T cell receptor beta
T cell receptor beta
TRBV1
        10        20        30        40        50        60
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS
        70        80        90       100       110
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSAAPDWGASAETLYFGSGTRLTVL

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. 1KJ2 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 1KJ2 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1KJ2 assembly 1  
Peptide only [cif]
  1. 1KJ2 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1kj2

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.