1ED3

Rano-A*av1 binding "ILFPSSERLISNR" at 2.55Å 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

1. Beta 2 microglobulin

['B', 'E']

2. Class I alpha
Rano-A*av1

['A', 'D']

3. Peptide
ILFPSSERLISNR

['C', 'F']

Species

Rattus norvegicus (Norway Rat)

Locus / Allele group

RANO-A / Rano-A*av1

Publication

Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa.

Speir JA, Stevens J, Joly E, Butcher GW, Wilson IA

Immunity (2001) 14, 81-92 [doi:10.1016/s1074-7613(01)00091-7] [pubmed:11163232]

The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. The antigenic structure of MTF-E was unpredictable due to its extraordinary length and two arginines that could serve as potential anchor residues. The crystal structure of RT1-Aa-MTF-E at 2.55 A shows that both peptide termini are anchored, as in other class I molecules, but the central residues in two independent pMHC complexes adopt completely different bulged conformations based on local environment. The MTF-E epitope is fully exposed within the putative T cell receptor (TCR) footprint. The flexibility demonstrated by the MTF-E structures illustrates how different TCRs may be raised against chemically identical, but structurally dissimilar, pMHC complexes.

Structure deposition and release

Deposited: 2000-01-26

Released: 2001-02-28

Revised: 2018-01-24

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: ILFPSSERLISNR

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 ILE

TYR59

TYR7

GLN63

TYR171

LEU5

THR163

TRP167

GLN62

TYR159

P10 ILE

ILE66

GLU69

TYR152

ARG155

ILE73

TRP70

P11 SER

TYR152

ARG155

ASP77

ILE73

TRP147

ALA150

P12 ASN

ASP77

ILE73

VAL76

LYS146

THR143

TRP147

P13 ARG

ASP116

LEU81

TRP147

TYR74

TYR123

ARG114

THR80

TYR84

ASP77

ILE95

LYS146

THR143

GLU97

P2 LEU

GLN63

ILE66

TYR159

THR163

ALA67

TRP70

TYR9

TYR7

MET45

TYR99

ALA24

P3 PHE

LEU156

TYR152

ARG155

TYR159

TRP70

TYR9

TYR7

TYR99

P4 PRO

GLU69

TRP70

TYR9

ILE66

P5 SER

THR163

GLN62

ILE66

P6 SER

GLN62

GLU69

ILE66

P7 GLU

ARG65

GLN62

ILE66

GLU69

P8 ARG

GLU69

P9 LEU

GLU69

TYR152

ARG155

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

GLN63

ILE66

TYR7

B Pocket

ALA24

VAL34

MET45

GLN63

ILE66

ALA67

TYR7

TRP70

TYR9

TYR99

C Pocket

TRP70

ILE73

TYR74

TYR9

GLU97

D Pocket

ARG114

ARG155

LEU156

TYR159

LEU160

TYR99

E Pocket

ARG114

TRP147

TYR152

LEU156

GLU97

F Pocket

ASP116

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 IQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDW 70 80 90 SFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM

2. Class I alpha Rano-Aav1 IPD-MHC* [ipd-mhc:RT108344]	10 20 30 40 50 60 GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYW 70 80 90 100 110 120 EQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDG 130 140 150 160 170 180 RDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLL 190 200 210 220 230 240 RSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWE

3. Peptide	ILFPSSERLISNR

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]

Components

MHC Class I alpha chain [cif]

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

Peptide only [cif]

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/1ed3

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.