6LBE

Ctid-UAA106 binding "FANFCLMMI" at 2.60Å 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', 'D']

2. Class I alpha
Ctid-UAA106

['A', 'C']

3. Peptide
FANFCLMMI

['E', 'F']

Species

Ctenopharyngodon idella (Grass carp)

Locus / Allele group

CTID-UAA / Ctid-UAA106

Publication

The Mechanism of ��2m Molecule-Induced Changes in the Peptide Presentation Profile in a Bony Fish.

Li Z, Zhang N, Ma L, Zhang L, Meng G, Xia C

iScience (2020) 23, 101119 [doi:10.1016/j.isci.2020.101119] [pubmed:32438322]

Contemporary antigen presentation knowledge is based on the existence of a single β2m locus, and a classical MHC class I forms a complex with a peptide (i.e., pMHC-I) to trigger CTL immunity. However, two β2m loci have been found in diploid bony fish; the function of the two β2m molecules is unclear. Here, we determined the variant peptide profiles originating from different products of the β2m loci binding to the same MHC-I molecule and further solved the crystal structures of the two pMHC-I molecules (i.e., pCtid-UAA-β2m-2 and pCtid-UAA-β2m-1-II). Of note, in pCtid-UAA-β2m-2, a unique hydrogen bond network formed in the bottom of the peptide-binding groove (PBG) led to α2-helix drift, ultimately leading to structural changes in the PBG. The mechanism of the change in peptide presentation profiles by β2m molecules is illustrated. The results are also of great significance for antivirus and antitumor functions in cold-blooded vertebrates and even humans.

Structure deposition and release

Deposited: 2019-11-14

Released: 2020-11-04

Revised: 2020-11-04

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: FANFCLMMI

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 PHE

VAL64

GLN61

ARG60

TYR57

TYR7

TYR167

TYR155

TRP163

PHE32

LEU5

P2 ALA

TYR155

TYR9

LEU65

VAL64

GLN61

TYR96

TYR7

P3 ASN

ASN152

TYR155

TYR9

TYR96

TYR110

GLN151

VAL64

P4 PHE

GLN151

VAL64

TYR110

P5 CYS

VAL71

TYR9

ALA68

ASN94

GLY67

TYR112

P6 LEU

VAL148

GLN151

P7 MET

LEU146

VAL148

LYS142

TRP143

VAL71

P8 MET

ILE78

ASP74

LYS142

TRP143

VAL71

SER75

P9 ILE

ARG82

PHE119

ILE78

TRP92

VAL79

ILE138

THR139

LYS142

TRP143

SER75

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]

Chain sequences

1. Beta 2 microglobulin Beta 2 microglobulin	10 20 30 40 50 60 MRQSDPKVQVYSRNPGEYGKANVLICYVSGFHPPDITIQLLKNGVEIPGSTQTDLAFEEG 70 80 90 WQFHLTKYVDFLPQPGEEYTCRVRHMSSPTKSYTWEPDM

2. Class I alpha Ctid-UAA106	10 20 30 40 50 60 GTHSLKYVYTGVSRGIDFPEFTAVGMVDDGQFMYFDSNSMKAVPKTEWIRQNEGADYWDR 70 80 90 100 110 120 QTQVLIGAHQVFKDSIQIVMERFNQSKGVHTWQNMYGCELNDDGTTQGFYQYAYDGEDFV 130 140 150 160 170 180 SLDKNTLTWTAANPQAVITKHKWEALAVAEQNKGYLENTCIEWLKKYVAYGKDTLERKVS 190 200 210 220 230 240 PQVSLLQKDPSSPVTCHATGFYPSGVTITWQKNGQDHDEDVDLGELLPNEDGSFQRMSTL 250 260 270 NVGPDEWKNNRFSCVVEHQDKTIRKTEDDIITNFD

3. Peptide	FANFCLMMI

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/6lbe

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.