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1QO3

H2-Dd binding "RGPGRAFVTI" with Ly49a NK receptor 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 and ly49a

1. Beta 2 microglobulin
['B']
2. Class I alpha
H2-Dd
['A']
3. Natural Killer Cell Receptor Ly49a
['C', 'D']
4. Peptide
RGPGRAFVTI
['P']

Species


Locus / Allele group


Publication

Crystal structure of a lectin-like natural killer cell receptor bound to its MHC class I ligand.

Tormo J, Natarajan K, Margulies DH, Mariuzza RA
Nature (1999) 402, 623-31 [doi:10.1038/45170]  [pubmed:10604468

The neuroactive mycotoxin lolitrem B causes a neurological syndrome in grazing livestock resulting in hyperexcitability, muscle tremors, ataxia and, in severe cases, clonic seizures and death. To define the effects of the major toxin lolitrem B in the brain, a functional metabolomic study was undertaken in which motor coordination and tremor were quantified and metabolomic profiling undertaken to determine relative abundance of both toxin and key neurotransmitters in various brain regions in male mice. Marked differences were observed in the duration of tremor and coordination between lolitrem B pathway members, with some showing protracted effects and others none at all. Lolitrem B was identified in liver, kidney, cerebral cortex and thalamus but not in brainstem or cerebellum which were hypothesised previously to be the primary site of action. Metabolomic profiling showed significant variation in specific neurotransmitter and amino acid profiles over time. This study demonstrates accumulation of lolitrem B in the brain, with non-detectable levels of toxin in the brainstem and cerebellum, inducing alterations in metabolites such as tyrosine, suggesting a dynamic catecholaminergic response over time. Temporal characterisation of key pathways in the pathophysiological response of lolitrem B in the brain were also identified.

Structure deposition and release

Deposited: 1999-11-01
Released: 2000-01-02
Revised: 2015-04-15

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Decamer (10 amino acids)

Sequence: RGPGRAFVTI

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 ARG

GLU163
LEU5
ARG62
TRP167
TYR7
TYR159
TYR59
ARG66
GLU58
TYR171
GLU63
P10 ILE

TYR123
TRP147
THR143
TYR84
ALA81
ILE142
LYS146
ASP77
THR80
P2 GLY

GLU63
GLU163
TYR7
TYR159
ARG66
P3 PRO

TYR7
ASN70
TRP97
TYR159
ARG66
ALA99
TRP114
P4 GLY

ARG66
TRP97
TRP114
ASN70
P5 ARG

ASN70
PHE74
SER73
TRP147
TRP97
PHE116
TRP114
ARG155
ASP77
P6 ALA

ARG155
ASN70
SER73
P7 PHE

GLN72
GLY69
SER73
P8 VAL

ALA152
ARG155
SER73
TRP147
P9 THR

TRP147
LYS146
ASP77
SER73
VAL76
THR143

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
GLU163
TRP167
TYR171
LEU5
TYR59
GLU63
ARG66
TYR7
B Pocket

GLU24
VAL34
TYR45
GLU63
ARG66
ALA67
TYR7
ASN70
VAL9
ALA99
C Pocket

ASN70
SER73
PHE74
VAL9
TRP97
D Pocket

TRP114
ARG155
ASP156
TYR159
LEU160
ALA99
E Pocket

TRP114
TRP147
ALA152
ASP156
TRP97
F Pocket

PHE116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
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
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

2. Class I alpha
H2-Dd
        10        20        30        40        50        60
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
        70        80        90       100       110       120
ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
       130       140       150       160       170       180
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
       190       200       210       220       230       240
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

3. Natural Killer Cell Receptor Ly49a
Natural Killer Cell Receptor Ly49a
        10        20        30        40        50        60
STVLDSLQHTGRGDKVYWFCYGMKCYYFVMDRKTWSGCKQTCQSSSLSLLKIDDEDELKF
        70        80        90       100       110       120
LQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTRKYNIRDGGCMLLSKTRLDNGNC
       130
DQVFICICGKRLDKFPH

4. Peptide
RGPGRAFVTI


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. 1QO3 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 1QO3 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1QO3 assembly 1  
Peptide only [cif]
  1. 1QO3 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1qo3

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