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1HYR

Non-classical MHC Class I molecule MICA with NKG2D at 2.70Å 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

Complex structure of the activating immunoreceptor NKG2D and its MHC class I-like ligand MICA.

Li P, Morris DL, Willcox BE, Steinle A, Spies T, Strong RK
Nat. Immunol. (2001) 2, 443-51 [doi:10.1038/87757]  [pubmed:11323699

To date, non-wear detection algorithms commonly employ a 30, 60, or even 90 mins interval or window in which acceleration values need to be below a threshold value. A major drawback of such intervals is that they need to be long enough to prevent false positives (type I errors), while short enough to prevent false negatives (type II errors), which limits detecting both short and longer episodes of non-wear time. In this paper, we propose a novel non-wear detection algorithm that eliminates the need for an interval. Rather than inspecting acceleration within intervals, we explore acceleration right before and right after an episode of non-wear time. We trained a deep convolutional neural network that was able to infer non-wear time by detecting when the accelerometer was removed and when it was placed back on again. We evaluate our algorithm against several baseline and existing non-wear algorithms, and our algorithm achieves a perfect precision, a recall of 0.9962, and an F1 score of 0.9981, outperforming all evaluated algorithms. Although our algorithm was developed using patterns learned from a hip-worn accelerometer, we propose algorithmic steps that can easily be applied to a wrist-worn accelerometer and a retrained classification model.

Structure deposition and release

Deposited: 2001-01-21
Released: 2001-05-23
Revised: 2011-07-13

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
DRETRDLTGNGKDLRMTLAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSQHFYYDGELFLS
       130       140       150       160       170       180
QNLETKEWTMPQSSRAQTLAMNVRNFLKEDAMKTKTHYHAMHADCLQELRRYLKSGVVLR
       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
NSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYS
        70        80        90       100       110       120
KEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGY
       130
IENCSTPNTYICMQRTV


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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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. 1HYR assembly 1  

Components

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

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1hyr

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