5UD8 Immune System date Dec 23, 2016
title Crystal Structure Of Mutant Ig-Like Domain
authors A.Sudom, X.Min, Z.Wang
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: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24
symmetry Space Group: P 2 21 21
R_factor 0.206 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
23.790 62.530 125.270 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 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] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (5ud8.pdb1.gz) 19 Kb
  • Biological Unit Coordinates (5ud8.pdb2.gz) 18 Kb
  • CSU: Contacts of Structural Units for 5UD8
  • Structure Factors (836 Kb)
  • Retrieve 5UD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UD8 from S2C, [Save to disk]
  • View 5UD8 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 5UD8
  • 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 5ud8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ud8_B] [5ud8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5UD8
  • Community annotation for 5UD8 at PDBWiki (http://pdbwiki.org)

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