5ELI Immune System date Nov 04, 2015
title Triggering Receptor Expressed On Myeloid Cells 2
authors T.J.Brett, D.L.Kober
compound source
Molecule: Triggering Receptor Expressed On Myeloid Cells 2
Chain: A, B
Synonym: Trem-2,Triggering Receptor Expressed On Monocytes
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trem2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_organ: Kidney
Expression_system_tissue: Embryonic Kidney
Expression_system_cell: Epithelial
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phlsec
symmetry Space Group: P 64 2 2
R_factor 0.261 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.763 125.763 183.659 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand NAG enzyme
Primary referenceNeurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms., Kober DL, Alexander-Brett JM, Karch CM, Cruchaga C, Colonna M, Holtzman MJ, Brett TJ, Elife. 2016 Dec 20;5. pii: e20391. doi: 10.7554/eLife.20391. PMID:27995897
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (5eli.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (5eli.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 5ELI
  • CSU: Contacts of Structural Units for 5ELI
  • Structure Factors (136 Kb)
  • Retrieve 5ELI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ELI from S2C, [Save to disk]
  • Re-refined 5eli structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5ELI in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5ELI
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5eli from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5eli_A] [5eli] [5eli_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ELI
  • Community annotation for 5ELI at PDBWiki (http://pdbwiki.org)

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