7FI7
Non-classical MHC Class I molecule MICA with NKG2D at 2.78Å 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. MICA
['C']
2. Natural Killer Cell Receptor NKG2d
['A', 'B']
Species
Locus / Allele group
Non-classical MHC Class I molecule
Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D
Cai, W., Peng, S., Xu, T., Tian, Y., Li, Y., Liu, J.
Structure deposition and release
Deposited: 2021-07-30
Released: 2022-08-31
Revised: 2022-08-31
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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1. MICA
MICA
|
10 20 30 40 50 60
MEPHSLRYNLTVLMWDGSVQSGFLTEVHLDGQPFLRCDRQKCRAKPQGQWAEDVLGNKTW 70 80 90 100 110 120 DRETRDLTGNGKDLRMTLAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSIHFYYDGELFLS 130 140 150 160 170 180 GNLETKEWTMPQSSRAQTLAMNVRNFWKEDAMKTKTHWHAMHADCLQELRRYLKSGVVLR 190 200 210 220 230 240 RTVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGNG 250 260 270 TYQTWVATRICQGEEQRFTCYMEHSGNHSTHPVPS |
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2. Natural Killer Cell Receptor NKG2d
Natural Killer Cell Receptor NKG2d
|
10 20 30 40 50 60
MENSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKV 70 80 90 100 110 120 YSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFK 130 GYIENCSTPNTYICMQRTV |
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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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.