5M02

H2-Db presenting "KAPFNFATM" to Alpha/Beta T cell receptor at 1.75Å 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.

Complex type

Class i with peptide and alpha beta tcr

1. Beta 2 microglobulin

['B']

2. Class I alpha
H2-Db

['A']

3. Peptide
KAPFNFATM

['P']

4. T cell receptor alpha
TRAV14

['G']

5. T cell receptor beta
TRBV13

['H']

Information on this structure on STCRdab.

Species

Mus musculus (Mouse)

Locus / Allele group

H2-D / H2-Db

Publication

Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant

Allerbring, E., Duru, A., Sun, R., Han, X., Uchtenhagen, H., Madhurantakam, C., Popov, A., Markova, N., Talyzina, A., Nygren, P.A., Sandalova, T., Achour, A.

Structure deposition and release

Deposited: 2016-10-03

Released: 2017-12-20

Revised: 2017-12-20

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Nonamer (9 amino acids)

Sequence: KAPFNFATM

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

TYR159

TYR7

TYR171

MET5

ARG62

TYR59

GLU63

TRP167

LYS66

GLU163

P2 ALA

TYR159

TYR7

TYR45

GLU63

LYS66

P3 PRO

TYR7

GLN70

LYS66

LEU114

SER99

TYR159

GLN97

GLU9

P4 PHE

TYR159

GLU163

GLN70

LYS66

TYR156

P5 ASN

PHE74

PHE116

TYR156

TRP73

GLN97

GLN70

P6 PHE

HIS155

TRP73

ALA152

TYR156

P7 ALA

SER150

LYS146

TRP73

TRP147

P8 THR

SER77

TRP73

TRP147

ASN80

VAL76

LYS146

P9 MET

SER77

ASN80

TYR123

LEU95

THR143

LEU81

TRP147

TRP73

ILE124

PHE116

ILE142

TYR84

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

GLU163

TRP167

TYR171

MET5

TYR59

GLU63

LYS66

TYR7

B Pocket

SER24

VAL34

TYR45

GLU63

LYS66

ALA67

TYR7

GLN70

GLU9

SER99

C Pocket

GLN70

TRP73

PHE74

GLU9

GLN97

D Pocket

LEU114

HIS155

TYR156

TYR159

LEU160

SER99

E Pocket

LEU114

TRP147

ALA152

TYR156

GLN97

F Pocket

PHE116

TYR123

THR143

LYS146

TRP147

SER77

ASN80

LEU81

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 MARSVTLVFLVLVSLTGLMGIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQML 70 80 90 100 110 KNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

2. Class I alpha H2-Db	10 20 30 40 50 60 GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW 70 80 90 100 110 120 ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG 130 140 150 160 170 180 RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

3. Peptide	KAPFNFATM

4. T cell receptor alpha T cell receptor alpha TRAV14	10 20 30 40 50 60 QQKEKHDQQQVRQSPQSLTVWEGGTTVLTCSYEDSTFNYFPWYQQFPGEGPALLISILSV 70 80 90 100 110 120 SDKKEDGRFTTFFNKREKKLSLHIIDSQPGDSATYFCAALYGNEKITFGAGTKLTIKPNI 130 140 150 160 170 180 QNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGA 190 200 IAWSNQTSFTCQDIFKETNATYPSS

5. T cell receptor beta T cell receptor beta TRBV13	10 20 30 40 50 60 AVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPD 70 80 90 100 110 120 GYKASRPSQENFSLILELASLSQTAVYFCASSDAGGRNTLYFGAGTRLSVLEDLRNVTPP 130 140 150 160 170 180 KVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYS 190 200 210 220 230 YSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADC

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]

5M02 assembly 1

Components

MHC Class I alpha chain [cif]

5M02 assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

5M02 assembly 1

Peptide only [cif]

5M02 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/5m02

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

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.