3VXS

HLA-A*24:02 presenting "RYPLTLGWCF" to Alpha/Beta T cell receptor at 1.80Å 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
HLA-A*24:02

['A']

3. Peptide
RYPLTLGWCF

['C']

4. T cell receptor alpha
TRAV21

['D']

5. T cell receptor beta
TRBV7

['E']

Information on this structure on STCRdab.

Species

Homo sapiens (Human)

Locus / Allele group

HLA-A / HLA-A*24

Publication

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection.

Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A

Sci Rep (2013) 3, 3097 [doi:10.1038/srep03097] [pubmed:24192765]

We investigated the crystal structure of an HLA-A*2402-restricted CTL epitope in the HIV-1 nef gene (Nef134-10) before (pHLA) or after TCR docking. The wild type epitope and two escape mutants were included in the study. Y135F was an early-appearing major mutation, while F139L was a late-appearing mutation which was selected in the patients without Y135F. F139 was an eminent feature of the Nef134-10 epitope. Wild type-specific TCR was less fit to F139L mutant suggesting that F139L is an escape from the CTL against the wild type epitope. Although Y135F mutation disrupted the hydrogen bond to HLA-A*2402 His70, newly formed hydrogen bond between T138 and His70 kept the conformation of the epitope in the reconstituted pMHC. TCR from Y135F- or dually-specific CTL had unique mode of binding to the mutant epitope. Y135F has been reported as a processing mutant but CTL carrying structurally adequate TCR can be found in the patients.

Structure deposition and release

Deposited: 2012-09-20

Released: 2013-10-23

Revised: 2013-11-20

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: RYPLTLGWCF

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

TYR159

TYR59

TYR7

ARG170

GLY167

TYR171

LYS66

THR163

GLU63

PHE33

MET5

ASP166

P10 PHE

TYR123

ASN77

ILE80

ALA81

TRP147

LEU95

ILE142

THR143

LYS146

TYR84

ILE124

TYR116

P2 TYR

LYS66

VAL67

TYR159

TYR7

HIS70

SER9

ALA24

THR163

PHE22

GLU63

MET45

PHE99

P3 PRO

PHE99

LYS66

TYR159

P4 LEU

GLN156

LYS66

P5 THR

HIS70

LYS66

THR73

ALA69

P6 LEU

GLN156

P7 GLY

VAL152

GLN156

TRP147

P8 TRP

ASP74

MET97

TYR116

THR73

TRP147

GLN156

HIS70

ASN77

PHE99

HIS114

P9 CYS

THR143

LYS146

GLU76

ILE80

TRP147

ASN77

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

ALA159

GLY163

ASP167

ARG171

SER5

GLU59

GLU63

GLY66

ARG7

B Pocket

ILE24

PHE34

ARG45

GLU63

GLY66

LYS67

ARG7

ALA70

PHE9

MET99

C Pocket

ALA70

GLN73

THR74

PHE9

GLN97

D Pocket

TYR114

GLU155

GLN156

ALA159

TYR160

MET99

E Pocket

TYR114

LYS147

HIS152

GLN156

GLN97

F Pocket

GLN116

ASP123

ILE143

ARG146

LYS147

GLU77

ARG80

ILE81

ARG84

THR95

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 MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha HLA-A24:02 IPD-IMGT/HLA* [ipd-imgt:HLA34790]	10 20 30 40 50 60 MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY 70 80 90 100 110 120 WDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYD 130 140 150 160 170 180 GKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETL 190 200 210 220 230 240 QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG 250 260 270 TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

3. Peptide	RYPLTLGWCF

4. T cell receptor alpha T cell receptor alpha TRAV21	10 20 30 40 50 60 MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS 70 80 90 100 110 120 GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVRMDSSYKLIFGSGTRLLVRPDIQNPDP 130 140 150 160 170 180 AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN 190 200 KSDFACANAFNNSIIPEDTFFPSPESS

5. T cell receptor beta T cell receptor beta TRBV7	10 20 30 40 50 60 MDTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSR 70 80 90 100 110 120 LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSSWDTGELFFGEGSRLTVLEDLKNV 130 140 150 160 170 180 FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ 190 200 210 220 230 240 PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW GRAD

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]

3VXS assembly 1

Components

MHC Class I alpha chain [cif]

3VXS assembly 1

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

3VXS assembly 1

Peptide only [cif]

3VXS assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/3vxs

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.