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6KWN

SLA-1*13:01 binding "NSDTVGWSW" at 2.40Å 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

1. Beta 2 microglobulin
['B']
2. Class I alpha
SLA-1*13:01
['A']
3. Peptide
NSDTVGWSW
['C']

Species


Locus / Allele group


Publication

Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism.

Wei X, Wang S, Li Z, Li Z, Qu Z, Wang S, Zou B, Liang R, Xia C, Zhang N
Front Immunol (2021) 12, 592447 [doi:10.3389/fimmu.2021.592447]  [pubmed:33717070

The micropolymorphism of major histocompatibility complex class I (MHC-I) can greatly alter the plasticity of peptide presentation, but elucidating the underlying mechanism remains a challenge. Here we investigated the impact of the micropolymorphism on peptide presentation of swine MHC-I (termed swine leukocyte antigen class I, SLA-I) molecules via immunopeptidomes that were determined by our newly developed random peptide library combined with the mass spectrometry (MS) de novo sequencing method (termed RPLD-MS) and the corresponding crystal structures. The immunopeptidomes of SLA-1*04:01, SLA-1*13:01, and their mutants showed that mutations of residues 156 and 99 could expand and narrow the ranges of peptides presented by SLA-I molecules, respectively. R156A mutation of SLA-1*04:01 altered the charge properties and enlarged the volume size of pocket D, which eliminated the harsh restriction to accommodate the third (P3) anchor residue of the peptide and expanded the peptide binding scope. Compared with 99Tyr of SLA-1*0401, 99Phe of SLA-1*13:01 could not form a conservative hydrogen bond with the backbone of the P3 residues, leading to fewer changes in the pocket properties but a significant decrease in quantitative of immunopeptidomes. This absent force could be compensated by the salt bridge formed by P1-E and 170Arg. These data illustrate two distinguishing manners that show how micropolymorphism alters the peptide-binding plasticity of SLA-I alleles, verifying the sensitivity and accuracy of the RPLD-MS method for determining the peptide binding characteristics of MHC-I in vitro and helping to more accurately predict and identify MHC-I restricted epitopes.

Structure deposition and release

Deposited: 2019-09-07
Released: 2020-09-09
Revised: 2021-03-24

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: NSDTVGWSW

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 ASN

LEU5
TYR7
SER167
TYR59
LYS66
TYR171
TYR159
LEU163
ARG170
GLU63
P2 SER

TYR159
LEU163
MET45
GLU63
TYR99
ASN70
TYR7
TYR9
LYS66
VAL67
P3 ASP

ASN70
TYR9
ARG114
ARG155
TYR159
LYS66
TYR99
ARG156
P4 THR

ARG156
ASN70
LYS66
P5 VAL

TYR9
THR73
ARG114
ASP69
TYR74
TYR99
ARG156
ASN70
P6 GLY

ARG156
ASN70
THR73
P7 TRP

THR73
LYS146
ARG156
VAL152
TRP147
ALA150
P8 SER

LYS146
THR80
TRP147
P9 TRP

TYR84
THR143
TYR123
TYR74
LYS146
LEU95
TRP147
ILE124
SER97
ILE142
LEU81
THR73
ARG114
GLY77
THR80
ASP116

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
LEU163
SER167
TYR171
LEU5
TYR59
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
ASN70
TYR9
TYR99
C Pocket

ASN70
THR73
TYR74
TYR9
SER97
D Pocket

ARG114
ARG155
ARG156
TYR159
LEU160
TYR99
E Pocket

ARG114
TRP147
VAL152
ARG156
SER97
F Pocket

ASP116
TYR123
THR143
LYS146
TRP147
GLY77
THR80
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
FVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDW
        70        80        90
SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

2. Class I alpha
SLA-1*13:01
        10        20        30        40        50        60
GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDNYAPNPRMEPRVPWIQQEGQDYW
        70        80        90       100       110       120
DEETRKVKDNAQTYGVGLNTLRGYYNQSEAGSHTLQSMYGCYLGPDGLLLHGYRQDAYDG
       130       140       150       160       170       180
ADYIALNEDLRSWTAADMAAQITKRKWEAANVAERRRSYLQGLCVESLRRYLEMGKDTLQ
       190       200       210       220       230       240
RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT
       250       260       270
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

3. Peptide
NSDTVGWSW


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]
  1. 6KWN assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6KWN assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6KWN assembly 1  
Peptide only [cif]
  1. 6KWN assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6kwn

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