Alpha This is a work in progress and may change. Your feedback is very welcome.
  


7TUC

HLA-B*44:05 binding "EEFGRAFSF" at 1.25Å 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*44:05
['A']
3. Peptide
EEFGRAFSF
['P']

Species

Locus / Allele group

HLA-B / HLA-B*44

Publication

Crystal structure of HLA-B*44:05 (T73C) with 9mer EEFGRAFSF

Jiang, J., Natarajan, K., Kim, E., Boyd, L.F., Margulies, D.H.

Structure deposition and release

Deposited: 2022-02-02
Released: 2022-09-07
Revised: 2022-09-28

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: EEFGRAFSF

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 GLU

SER167
MET5
GLU63
TYR171
TYR159
TYR59
TYR7
LEU163
ARG62
ARG170
 P2 GLU

SER67
TYR9
THR24
LEU163
LYS45
TYR99
ILE66
ASN70
GLU63
TYR159
TYR7
 P3 PHE

TYR159
ASP156
ARG97
TYR9
ILE66
GLN155
TYR99
 P4 GLY

ILE66
 P5 ARG

GLN155
 P6 ALA

ASN70
CYS73
 P7 PHE

TRP147
CYS73
VAL152
GLN155
ASN77
ASP156
 P8 SER

CYS73
ASN77
THR143
LYS146
TRP147
 P9 PHE

TYR123
THR143
THR80
LYS146
TYR116
ALA81
TRP147
ASN77
TYR84
ILE95
ILE142
TYR74

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
MET5
TYR59
GLU63
ILE66
TYR7
B Pocket

THR24
VAL34
LYS45
GLU63
ILE66
SER67
TYR7
ASN70
TYR9
TYR99
C Pocket

ASN70
CYS73
TYR74
TYR9
ARG97
D Pocket

ASP114
GLN155
ASP156
TYR159
LEU160
TYR99
E Pocket

ASP114
TRP147
VAL152
ASP156
ARG97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-B*44:05
IPD-IMGT/HLA
[ipd-imgt:HLA30859]
        10        20        30        40        50        60
GSHSMRYFYTAMSRPGRGEPRFITVGYVDDTLFVRFDSDATSPRKEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DRETQISKTNTQCYRENLRTALRYYNQSEAGSHIIQRMYGCDVGPDGRLLRGYDQYAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQDRAYLEGLCVESLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPISDHEVTLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW
3. Peptide
EEFGRAFSF

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.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
   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. 7TUC assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7TUC assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7TUC assembly 1  
Peptide only [cif]
  1. 7TUC assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7tuc

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.