5UD7 Signaling Protein date Dec 23, 2016
title Crystal Structure Of Wild-Type Ig-Like Domain
authors A.Sudom, X.Min, Z.Wang
compound source
Molecule: Triggering Receptor Expressed On Myeloid Cells 2
Chain: A, B, C, D, E, F
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: Hek 293
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptt5
symmetry Space Group: P 41 21 2
R_factor 0.241 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
160.664 160.664 86.574 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
Primary referenceMolecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2., Sudom A, Talreja S, Danao J, Bragg E, Kegel R, Min X, Sharkov N, Marcora E, Thibault S, Bradley J, Wood S, Lim AC, Chen H, Wang S, Foltz IN, Sambashivan S, Wang Z, J Biol Chem. 2018 May 24. pii: RA118.002352. doi: 10.1074/jbc.RA118.002352. PMID:29794134
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (5ud7.pdb1.gz) 106 Kb
  • CSU: Contacts of Structural Units for 5UD7
  • Structure Factors (2422 Kb)
  • Retrieve 5UD7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UD7 from S2C, [Save to disk]
  • View 5UD7 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 5UD7
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ud7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ud7_D] [5ud7_E] [5ud7_A] [5ud7_F] [5ud7_B] [5ud7_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5UD7
  • Community annotation for 5UD7 at PDBWiki (http://pdbwiki.org)

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