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7FI5

Non-classical MHC Class I molecule MICA with NKG2D at 2.39Å 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

Mica with nkg2d

1. MICA
['C']
2. Natural Killer Cell Receptor NKG2d
['A', 'B']

Species


Locus / Allele group

Non-classical MHC Class I molecule

Publication

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


Chain sequences

1. MICA
MICA
        10        20        30        40        50        60
MEPHSLRYNLTVLSWDGSVQSGFLTEVHLDGQPFLRCDRQKCRAKPQGQWAEDVLGNKTW
        70        80        90       100       110       120
DRETRDLTGNGKDLRMTLAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSHHFYYDGELFLS
       130       140       150       160       170       180
WNLETKEFTMPQSSRAQTLAMNVRNFWKEDAMKTKTHFHAMHADCLQELRRYLKSGVVLR
       190       200       210       220       230       240
RTVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGNG
       250       260       270
TYQTWVATRICQGEEQRFTCYMEHSGNHSTHPVPS

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.

Complete structures

Aligned structures [cif]
  1. 7FI5 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7FI5 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7FI5 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7fi5

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