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- PDB-5ud8: Crystal Structure of Mutant Ig-like Domain -

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Basic information

Entry
Database: PDB / ID: 5ud8
TitleCrystal Structure of Mutant Ig-like Domain
ComponentsTriggering receptor expressed on myeloid cells 2
KeywordsIMMUNE SYSTEM / Ig-like domain
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 / respiratory burst after phagocytosis / positive regulation of macrophage fusion / import into cell / sulfatide binding / positive regulation of engulfment of apoptotic cell / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of fat cell proliferation / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / lipoteichoic acid binding / regulation of intracellular signal transduction / positive regulation of establishment of protein localization / positive regulation of synapse pruning / microglial cell activation involved in immune response / very-low-density lipoprotein particle binding / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of astrocyte activation / apolipoprotein A-I binding / positive regulation of low-density lipoprotein particle clearance / positive regulation of microglial cell migration / negative regulation of autophagic cell death / Other semaphorin interactions / CXCL12-activated CXCR4 signaling pathway / detection of lipopolysaccharide / high-density lipoprotein particle binding / negative regulation of p38MAPK cascade / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / low-density lipoprotein particle binding / regulation of resting membrane potential / negative regulation of glial cell apoptotic process / cellular response to oxidised low-density lipoprotein particle stimulus / dendritic cell differentiation / complement-mediated synapse pruning / microglial cell proliferation / regulation of TOR signaling / negative regulation of NLRP3 inflammasome complex assembly / positive regulation of microglial cell activation / cellular response to lipoprotein particle stimulus / amyloid-beta clearance by cellular catabolic process / phagocytosis, recognition / semaphorin receptor complex / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of phagocytosis, engulfment / cellular response to peptidoglycan / positive regulation of chemotaxis / peptidoglycan binding / cellular response to lipid / positive regulation of proteasomal protein catabolic process / positive regulation of amyloid-beta clearance / kinase activator activity / phosphatidylethanolamine binding / positive regulation of kinase activity / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / apoptotic cell clearance / regulation of interleukin-6 production / dendritic spine maintenance / negative regulation of interleukin-1 beta production / negative regulation of sequestering of triglyceride / phagocytosis, engulfment / pyroptotic inflammatory response / regulation of innate immune response / positive regulation of ATP biosynthetic process / negative regulation of cholesterol storage / phosphatidylserine binding / regulation of cytokine production involved in inflammatory response / plasma membrane raft / lipid homeostasis / apolipoprotein binding / lipoprotein particle binding / cellular response to lipoteichoic acid / amyloid-beta clearance / social behavior / positive regulation of interleukin-10 production / humoral immune response / regulation of lipid metabolic process / negative regulation of tumor necrosis factor production / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of TOR signaling / positive regulation of cholesterol efflux / negative regulation of cytokine production involved in inflammatory response / response to axon injury / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / regulation of peptidyl-tyrosine phosphorylation / positive regulation of calcium-mediated signaling
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
Triggering receptor expressed on myeloid cells 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triggering receptor expressed on myeloid cells 2
B: Triggering receptor expressed on myeloid cells 2


Theoretical massNumber of molelcules
Total (without water)25,0602
Polymers25,0602
Non-polymers00
Water2,036113
1
A: Triggering receptor expressed on myeloid cells 2


Theoretical massNumber of molelcules
Total (without water)12,5301
Polymers12,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triggering receptor expressed on myeloid cells 2


Theoretical massNumber of molelcules
Total (without water)12,5301
Polymers12,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.790, 62.530, 125.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 12530.212 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREM2 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.84 % / Mosaicity: 0.59 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8 / Details: 30% PEG 6000, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2013 / Details: 3X3 CCD ARRAY
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.25 Å / Num. obs: 17947 / % possible obs: 98.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.93.90.351193.6
5.69-44.2560.09199.7

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6
RfactorNum. reflection% reflection
Rfree0.248 913 5.1 %
Rwork0.2057 --
obs0.2079 17894 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 46.2 Å2 / Biso mean: 11.43 Å2 / Biso min: 1.07 Å2
Refinement stepCycle: final / Resolution: 1.8→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 0 113 1744
Biso mean---14.31 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061668
X-RAY DIFFRACTIONf_angle_d1.0972259
X-RAY DIFFRACTIONf_chiral_restr0.083261
X-RAY DIFFRACTIONf_plane_restr0.004285
X-RAY DIFFRACTIONf_dihedral_angle_d15.993588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.89490.25561190.22072214233392
1.8949-2.01360.25541300.20382359248998
2.0136-2.16910.22931370.19062408254599
2.1691-2.38740.2381210.211324412562100
2.3874-2.73280.32191440.220924202564100
2.7328-3.44280.23251270.21425122639100
3.4428-44.26580.22631350.193726272762100

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