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3JTT

Mamu-A1*002:01 binding "YTSGPGIRY" at 2.80Å 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', 'E', 'H']
2. Class I alpha
Mamu-A1*002:01
['A', 'D', 'G']
3. Peptide
YTSGPGIRY
['C', 'F', 'I']

Species


Locus / Allele group


Publication

Crystal structure of Rhesus macaque MHC class I:Mamu-A*02

Dai, L.

Structure deposition and release

Deposited: 2009-09-14
Released: 2010-09-15
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: YTSGPGIRY

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 TYR

TRP167
TYR159
TYR59
TYR7
ARG62
TYR99
GLU163
GLU63
MET5
TYR171
P2 THR

TYR9
ARG62
ASN66
MET45
TYR7
TYR99
GLU63
MET67
TYR159
P3 SER

TYR9
ARG62
ASN66
GLU70
HIS156
TYR99
TYR159
P4 GLY

ASN66
ARG97
GLU70
ARG62
P5 PRO

ASN66
ARG97
GLU70
ALA69
ASN73
P6 GLY

ASN73
GLU152
P7 ILE

GLU152
TRP147
ALA150
LYS146
P8 ARG

TRP147
ASN77
VAL76
LYS146
ASN73
THR143
ASN80
P9 TYR

TRP147
THR143
ASN142
LEU81
ASN77
ILE124
ASN80
ILE95
LYS146
GLN96
TYR84
TYR123
ARG97
SER116

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
MET5
TYR59
GLU63
ASN66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
ASN66
MET67
TYR7
GLU70
TYR9
TYR99
C Pocket

GLU70
ASN73
ALA74
TYR9
ARG97
D Pocket

HIS114
GLN155
HIS156
TYR159
LEU160
TYR99
E Pocket

HIS114
TRP147
GLU152
HIS156
ARG97
F Pocket

SER116
TYR123
THR143
LYS146
TRP147
ASN77
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
MIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

2. Class I alpha
Mamu-A1*002:01
        10        20        30        40        50        60
GSHSMRYFYTSMSRPGRWEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWVEQEGPEYW
        70        80        90       100       110       120
DRETRNMKAETQNAPVNLRNLRGYYNQSEAGSHTIQRMYGCDLGPDGRLLRGYHQSAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWTAADMAAQNTQRKWEAAGEAEQHRTYLEGECLEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPVSDQEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGKEQRYTCHVQHEGLREPLTLRWEP

3. Peptide
YTSGPGIRY


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

Data can be downloaded to your local machine from the links below.
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   e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 3JTT assembly 1  
  2. 3JTT assembly 2  
  3. 3JTT assembly 3  

Components

MHC Class I alpha chain [cif]
  1. 3JTT assembly 1  
  2. 3JTT assembly 2  
  3. 3JTT assembly 3  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3JTT assembly 1  
  2. 3JTT assembly 2  
  3. 3JTT assembly 3  
Peptide only [cif]
  1. 3JTT assembly 1  
  2. 3JTT assembly 2  
  3. 3JTT assembly 3  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3jtt

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