7TUE
HLA-B*44:05 with Tapasin at 3.10Å 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
1. Beta 2 microglobulin
['B']
2. Class I alpha
HLA-B*44:05
HLA-B*44:05
['A']
3. Tapasin
['D']
Species
Locus / Allele group
Crystal structure of Tapasin in complex with HLA-B*44:05 (T73C)
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 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.
|
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. Tapasin
Tapasin
|
10 20 30 40 50 60
GPAVIECWFVEDASGKGLAKRPGALLLRQGPGEPPPRPDLDPELYLSVHDPAGALQAAFR 70 80 90 100 110 120 RYPRGAPAPHCEMSRFVPLPASAKWASGLTPAQNCPRALDGAWLMVSISSPVLSLSSLLR 130 140 150 160 170 180 PQPEPQQEPVLITMATVVLTVLTHTPAPRVRLGQDALLDLSFAYMPPTSEAASSLAPGPP 190 200 210 220 230 240 PFGLEWRRQHLGKGHLLLAATPGLNGQMPAAQEGAVAFAAWDDDEPWGPWTGNGTFWLPR 250 260 270 280 290 300 VQPFQEGTYLATIHLPYLQGQVTLELAVYKPPKVSLMPATLARAAPGEAPPELLCLVSHF 310 320 330 340 350 360 YPSGGLEVEWELRGGPGGRSQKAEGQRWLSALRHHSDGSVSLSGHLQPPPVTTEQHGARY 370 380 390 400 410 ACRIHHPSLPASGRSAEVTLEGGLEVLFQGPGGGLNDIFEAQKIEWHEGGHHHHHH |
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.
Components
MHC Class I alpha chain [cif]
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
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
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
This work is licensed under a Creative Commons Attribution 4.0 International License.