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- PDB-5ud7: Crystal Structure of Wild-Type Ig-like Domain -

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Basic information

Entry
Database: PDB / ID: 5ud7
TitleCrystal Structure of Wild-Type Ig-like Domain
ComponentsTriggering receptor expressed on myeloid cells 2
KeywordsSIGNALING PROTEIN / Ig-like domain / receptor / lipid binding / immunoregulatory
Function / homology
Function and homology information


positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of inward rectifier potassium channel activity / positive regulation of C-C chemokine receptor CCR7 signaling pathway / positive regulation of CAMKK-AMPK signaling cascade ...positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of inward rectifier potassium channel activity / positive regulation of C-C chemokine receptor CCR7 signaling pathway / positive regulation of CAMKK-AMPK signaling cascade / excitatory synapse pruning / positive regulation of CD40 signaling pathway / negative regulation of cell activation / detection of peptidoglycan / positive regulation of macrophage fusion / import into cell / negative regulation of macrophage colony-stimulating factor signaling pathway / sulfatide binding / positive regulation of engulfment of apoptotic cell / regulation of intracellular signal transduction / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / negative regulation of fat cell proliferation / lipoteichoic acid binding / positive regulation of establishment of protein localization / positive regulation of synapse pruning / microglial cell activation involved in immune response / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of astrocyte activation / apolipoprotein A-I binding / respiratory burst after phagocytosis / positive regulation of low-density lipoprotein particle clearance / positive regulation of microglial cell migration / : / negative regulation of autophagic cell death / detection of lipopolysaccharide / Other semaphorin interactions / CXCL12-activated CXCR4 signaling pathway / very-low-density lipoprotein particle binding / negative regulation of p38MAPK cascade / high-density lipoprotein particle binding / negative regulation of neuroinflammatory response / negative regulation of glial cell apoptotic process / negative regulation of toll-like receptor 4 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / regulation of resting membrane potential / dendritic cell differentiation / negative regulation of NLRP3 inflammasome complex assembly / microglial cell proliferation / complement-mediated synapse pruning / positive regulation of microglial cell activation / low-density lipoprotein particle binding / regulation of TOR signaling / amyloid-beta clearance by cellular catabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of phagocytosis, engulfment / positive regulation of chemotaxis / cellular response to peptidoglycan / phagocytosis, recognition / peptidoglycan binding / positive regulation of proteasomal protein catabolic process / positive regulation of amyloid-beta clearance / phosphatidylethanolamine binding / kinase activator activity / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / positive regulation of kinase activity / cellular response to lipid / apoptotic cell clearance / regulation of interleukin-6 production / negative regulation of interleukin-1 beta production / dendritic spine maintenance / negative regulation of sequestering of triglyceride / phagocytosis, engulfment / positive regulation of ATP biosynthetic process / regulation of innate immune response / phosphatidylserine binding / pyroptotic inflammatory response / negative regulation of cholesterol storage / regulation of cytokine production involved in inflammatory response / plasma membrane raft / lipid homeostasis / lipoprotein particle binding / cellular response to lipoteichoic acid / apolipoprotein binding / positive regulation of interleukin-10 production / social behavior / humoral immune response / negative regulation of tumor necrosis factor production / regulation of lipid metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of TOR signaling / response to axon injury / positive regulation of cholesterol efflux / negative regulation of cytokine production involved in inflammatory response / positive regulation of calcium-mediated signaling / negative regulation of canonical NF-kappaB signal transduction / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phagocytosis / negative regulation of inflammatory response to antigenic stimulus / negative regulation of autophagy
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Triggering receptor expressed on myeloid cells 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.20002253654 Å
Model detailsIg-like Domain
AuthorsSudom, A. / Min, X. / Wang, Z.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Molecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2.
Authors: Sudom, A. / Talreja, S. / Danao, J. / Bragg, E. / Kegel, R. / Min, X. / Richardson, J. / Zhang, Z. / Sharkov, N. / Marcora, E. / Thibault, S. / Bradley, J. / Wood, S. / Lim, A.C. / Chen, H. ...Authors: Sudom, A. / Talreja, S. / Danao, J. / Bragg, E. / Kegel, R. / Min, X. / Richardson, J. / Zhang, Z. / Sharkov, N. / Marcora, E. / Thibault, S. / Bradley, J. / Wood, S. / Lim, A.C. / Chen, H. / Wang, S. / Foltz, I.N. / Sambashivan, S. / Wang, Z.
History
DepositionDec 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triggering receptor expressed on myeloid cells 2
B: Triggering receptor expressed on myeloid cells 2
C: Triggering receptor expressed on myeloid cells 2
D: Triggering receptor expressed on myeloid cells 2
E: Triggering receptor expressed on myeloid cells 2
F: Triggering receptor expressed on myeloid cells 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,88718
Polymers114,8306
Non-polymers2,05812
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.664, 160.664, 86.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein
Triggering receptor expressed on myeloid cells 2 / TREM-2 / Triggering receptor expressed on monocytes 2


Mass: 19138.254 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREM2 / Plasmid: pTT5 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q9NZC2
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 % / Mosaicity: 0.13 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.9
Details: 0.2 M sodium iodide, 1.6 M ammonium sulfate, 0.1 M Tris 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.4930209421 Å / Num. obs: 57945 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 42.4850452186 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.266 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.2627.63.5350.4591100
9.59-47.4919.70.0590.999199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.595
Highest resolutionLowest resolution
Rotation47.49 Å2.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UD8

5ud8


Resolution: 2.20002253654→47.4930209421 Å / SU ML: 0.291696042338 / Cross valid method: FREE R-VALUE / σ(F): 1.34350982755 / Phase error: 28.6067442793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277484697973 2944 5.08638562543 %
Rwork0.24082559937 54936 -
obs0.242745918946 57880 99.9982723173 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.0060292847 Å2
Refinement stepCycle: LAST / Resolution: 2.20002253654→47.4930209421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 94 151 5304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00855722462055263
X-RAY DIFFRACTIONf_angle_d1.009533322347154
X-RAY DIFFRACTIONf_chiral_restr0.0582289866674828
X-RAY DIFFRACTIONf_plane_restr0.00565807987661891
X-RAY DIFFRACTIONf_dihedral_angle_d11.20199064423061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23610.334089583761240.3037415302262579X-RAY DIFFRACTION100
2.2361-2.27460.402128532351590.2953333920982560X-RAY DIFFRACTION100
2.2746-2.3160.3592745672241340.28830209762575X-RAY DIFFRACTION100
2.316-2.36060.2961606359281360.2747894140022580X-RAY DIFFRACTION100
2.3606-2.40870.3361047895421350.2787693182122594X-RAY DIFFRACTION100
2.4087-2.46110.3120830176071300.2655620510362600X-RAY DIFFRACTION100
2.4611-2.51840.3115784213061420.2639040460332547X-RAY DIFFRACTION100
2.5184-2.58130.3014650905791440.2681059458982590X-RAY DIFFRACTION100
2.5813-2.65110.3030159185281250.2654046069162599X-RAY DIFFRACTION100
2.6511-2.72910.3260222161671380.2688180849472601X-RAY DIFFRACTION100
2.7291-2.81720.3552699811671360.2726283559152599X-RAY DIFFRACTION100
2.8172-2.91790.3323767705171460.286419465062602X-RAY DIFFRACTION100
2.9179-3.03470.3198355170581430.2669374092922585X-RAY DIFFRACTION100
3.0347-3.17280.2962505030111310.2549336745542604X-RAY DIFFRACTION100
3.1728-3.340.2621319984721500.245672677592631X-RAY DIFFRACTION100
3.34-3.54920.2624707142921270.226778338932614X-RAY DIFFRACTION100
3.5492-3.82310.2867725838551490.2175398611032639X-RAY DIFFRACTION100
3.8231-4.20770.2311160603941420.2058571870522645X-RAY DIFFRACTION100
4.2077-4.8160.2069904413081460.1845153909832664X-RAY DIFFRACTION100
4.816-6.06570.2331481923021490.2202402905662694X-RAY DIFFRACTION100
6.0657-47.50410.2920710540341580.2685375096442834X-RAY DIFFRACTION99.966588707

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