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1A1N

HLA-B*35:01 binding "VPLRPMTY" at 2.00Å 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*35:01
['A']
3. Peptide
VPLRPMTY
['C']

Species

Locus / Allele group

HLA-B / HLA-B*35

Publication

An altered position of the alpha 2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501.

Smith KJ, Reid SW, Stuart DI, McMichael AJ, Jones EY, Bell JI
Immunity (1996) 4, 203-13 [doi:10.1016/s1074-7613(00)80429-x]  [pubmed:8624811] 

The crystal structure of the human major histocompatibility complex class I B allele HLA B*3501 complexed with the 8-mer peptide epitope HIV1 Nef 75-82 (VPLRPMTY) has been determined at 2.0 angstrom resolution. Comparison with the crystal structure of the closely related allele HLA B*5301 reveals the structural basis for the tyrosine specificity of the B*3501 F pocket. The structure also reveals a novel conformation of the 8-mer peptide within the binding groove. The positions of the peptide N and C termini are nonstandard, but the classic pattern of hydrogen bonding to nonpolymorphic MHC class I residues is maintained, at the N terminus by addition of a water molecule, and at the C terminus by a substantial shift in the alpha 2 helix.

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: Octamer (8 amino acids)

Sequence: VPLRPMTY

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 VAL

TYR159
TRP167
TYR59
TYR7
ARG62
TYR171
LEU163
ASN63
 P2 PRO

TYR7
TYR9
ILE66
TYR99
ASN63
PHE67
TYR159
 P3 LEU

ARG97
ILE66
LEU156
TYR159
TYR9
ASN70
ASP114
TYR99
GLN155
 P4 ARG

ARG62
ILE66
LEU163
TYR159
 P5 PRO

THR73
ILE66
ASN70
THR69
 P6 MET

SER77
ARG97
THR73
VAL152
TRP147
 P7 THR

SER77
GLU76
LYS146
THR73
ASN80
TRP147
 P8 TYR

SER77
ILE124
GLN96
ILE95
LEU81
TYR123
TYR74
LYS146
THR143
ARG97
TYR84
ASN80
TRP147
SER116
ILE142

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
SER77
ASN80
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
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-B*35:01
IPD-IMGT/HLA
[ipd-imgt:HLA34423]
        10        20        30        40        50        60
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRPPWIEQEGPEYW
        70        80        90       100       110       120
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
3. Peptide
VPLRPMTY

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. 1A1N assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 1A1N assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1A1N assembly 1  
Peptide only [cif]
  1. 1A1N assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1a1n

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.