Mouse Non-classical MHC Class I molecule H2-T22 at 2.50Å resolution
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Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the gammadelta T-cell ligand T10.
T10 is a non-classical class Ib-like major histocompatibility complex (MHC) cell-surface antigen which binds directly to certain gammadelta T-cell receptors in the absence of any exogenous and endogenous ligands, such as peculiar lipids or glycolipids. The crystal structure at 2.5 A resolution of murine T10 was determined by molecular replacement using data from an almost perfectly twinned monoclinic crystal. The space group is P2(1), with unit-cell parameters a = 78.2, b = 70.0, c = 139.2 A, beta = 106.8 degrees. Self-rotation function analysis and various intensity statistics revealed the presence of pseudo-merohedral twinning, but these tests underestimated the true twin fraction of alpha approximately 0.46. Native Patterson analyses pointed to the presence of pseudo-translation among the four molecules present in the asymmetric unit. Data analysis, structure determination and model refinement are discussed.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
1. Beta 2 microglobulin
Beta 2 microglobulin
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10 20 30 40 50 60
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW 70 80 90 SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. H2-T22
H2-T22
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10 20 30 40 50 60
GSHSLRYFYTAVSRPGLGEPWFIIVGYVDDMQVLRFSSKEETPRMAPWLEQEEADDWEQQ 70 80 90 100 110 120 THIVTIQGQLSERNLMTLVHFYNKSMDDSHTLQWLQDCDVEPDRHLCLWYNQLAYDSEDL 130 140 150 160 170 180 PTLSENPSSCTVGNSTVPQISQHLEGHCSDVLQKYLEKGKERLLRSDPPKAHVTRHPRPE 190 200 210 220 230 240 GDVTLRCWALGFYPADITLTWQKDGEELTQDVEFVETRPAGDGTFQKWAAVVVPLGKVQS 250 YTCHVDHEGLPEPLTLRWEP |
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.
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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
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