1Q8M Immune System Receptor date Aug 21, 2003
title Crystal Structure Of The Human Myeloid Cell Activating Receptor Trem-1
authors S.Radaev, M.Kattah, B.Rostro, M.Colonna, P.D.Sun
compound source
Molecule: Triggering Receptor Expressed On Myeloid Cells 1
Chain: A, B, C, D
Fragment: Extracellular Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trem1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.315 128.595 62.389 90.00 101.69 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand GSH, SO4 enzyme
related structures by homologous chain: 1SMO
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structure of the human myeloid cell activating receptor TREM-1., Radaev S, Kattah M, Rostro B, Colonna M, Sun PD, Structure (Camb) 2003 Dec;11(12):1527-35. PMID:14656437
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1q8m.pdb1.gz) 44 Kb
  • Biological Unit Coordinates (1q8m.pdb2.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 1Q8M
  • CSU: Contacts of Structural Units for 1Q8M
  • Likely Quarternary Molecular Structure file(s) for 1Q8M
  • Structure Factors (295 Kb)
  • Retrieve 1Q8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q8M from S2C, [Save to disk]
  • Re-refined 1q8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Q8M 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 1Q8M
  • 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
  • 3D motif for 1Q8M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q8ma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1q8mb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1q8mc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1q8md_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1q8m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1q8m_C] [1q8m_B] [1q8m] [1q8m_D] [1q8m_A]
  • SWISS-PROT database: [Q9NP99]
  • Domain organization of [TREM1_HUMAN] by SWISSPFAM
  • Domain found in 1Q8M: [IG ] by SMART
  • Other resources with information on 1Q8M
  • Community annotation for 1Q8M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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