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1A1O

HLA-B*53:01 binding "KPIVQYDNF" at 2.30Å 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
HLA-B*53:01
['A']
3. Peptide
KPIVQYDNF
['C']

Species

Locus / Allele group

HLA-B / HLA-B*53

Publication

Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53.

Smith KJ, Reid SW, Harlos K, McMichael AJ, Stuart DI, Bell JI, Jones EY
Immunity (1996) 4, 215-28 [doi:10.1016/s1074-7613(00)80430-6]  [pubmed:8624812] 

The structure of the human MHC class I molecule HLA-B53 complexed to two nonameric peptide epitopes (from the malaria parasite P. falciparum and the HIV2 gag protein) has been determined by X-ray crystallography at 2.3 angstrom resolution. The structures reveal the architecture of a Pro-specific B pocket common to many HLA-B alleles. Relative to other alleles, the B53 peptide-binding groove is widened by a significant (up to 1.25 angstrom) shift in the position of the alpha 1 helix. Within this groove, bound water molecules, acting in concert with the side chains of polymorphic residues, provide the functional malleability of the MHC, which enables the high affinity/low specificity binding of multiple peptide epitopes.

Structure deposition and release

Deposited: 1997-12-11
Released: 1998-04-08
Revised: 2011-07-13

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: KPIVQYDNF

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

TRP167
PHE33
ARG62
ASN63
MET5
TYR171
TYR159
TYR59
TYR7
 P2 PRO

ILE66
PHE67
TYR7
ASN63
TYR9
TYR99
TYR159
 P3 ILE

TYR159
ILE66
ARG97
GLN155
LEU156
ASN70
TYR9
TYR99
 P4 VAL

ILE66
GLN155
ARG62
 P5 GLN

ARG97
GLN155
VAL152
LEU156
ASN70
 P6 TYR

THR69
ILE66
THR73
ASN70
GLN65
 P7 ASP

GLN155
VAL152
ALA150
TRP147
THR73
ASN77
 P8 ASN

THR143
GLU76
ILE80
LYS146
TRP147
THR73
ASN77
 P9 PHE

TRP147
ILE142
ASN77
ALA81
ILE95
THR143
TYR84
ILE80
LYS146
SER116
TYR123

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
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
B Pocket

ALA24
VAL34
THR45
ASN63
ILE66
PHE67
TYR7
ASN70
TYR9
TYR99
C Pocket

ASN70
THR73
TYR74
TYR9
ARG97
D Pocket

ASP114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

ASP114
TRP147
VAL152
LEU156
ARG97
F Pocket

SER116
TYR123
THR143
LYS146
TRP147
ASN77
ILE80
ALA81
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
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-B*53:01
IPD-IMGT/HLA
[ipd-imgt:HLA34760]
        10        20        30        40        50        60
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRPPWIEQEGPEYW
        70        80        90       100       110       120
DRNTQIFKTNTQTYRENLRIALRYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
3. Peptide
KPIVQYDNF

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. 1A1O assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 1A1O assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1A1O assembly 1  
Peptide only [cif]
  1. 1A1O assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1a1o

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.