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- PDB-6xds: Crystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-... -

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Basic information

Entry
Database: PDB / ID: 6xds
TitleCrystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-((4-bromophenyl)amino)ethan-1-ol
ComponentsSugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2
KeywordsSIGNALING PROTEIN / Trem2 / MBP / crystallization / chaperone
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 C-C chemokine receptor CCR7 signaling pathway / excitatory synapse pruning / positive regulation of CD40 signaling pathway ...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 C-C chemokine receptor CCR7 signaling pathway / excitatory synapse pruning / positive regulation of CD40 signaling pathway / negative regulation of triglyceride storage / negative regulation of cell activation / detection of peptidoglycan / positive regulation of macrophage fusion / import into cell / sulfatide binding / negative regulation of macrophage colony-stimulating factor signaling pathway / 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 engulfment of apoptotic cell / 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 / positive regulation of CAMKK-AMPK signaling cascade / negative regulation of autophagic cell death / respiratory burst after phagocytosis / positive regulation of low-density lipoprotein particle clearance / negative regulation of astrocyte activation / semaphorin receptor binding / positive regulation of microglial cell migration / apolipoprotein A-I binding / Other semaphorin interactions / detection of lipopolysaccharide / CXCL12-activated CXCR4 signaling pathway / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of neuroinflammatory response / high-density lipoprotein particle binding / negative regulation of p38MAPK cascade / negative regulation of glial cell apoptotic process / very-low-density lipoprotein particle binding / cellular response to oxidised low-density lipoprotein particle stimulus / complement-mediated synapse pruning / dendritic cell differentiation / microglial cell proliferation / negative regulation of NLRP3 inflammasome complex assembly / semaphorin receptor complex / positive regulation of microglial cell activation / regulation of TOR signaling / low-density lipoprotein particle binding / phagocytosis, recognition / amyloid-beta clearance by cellular catabolic process / cellular response to lipoprotein particle stimulus / regulation of resting membrane potential / positive regulation of phagocytosis, engulfment / cellular response to peptidoglycan / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / peptidoglycan binding / positive regulation of amyloid-beta clearance / positive regulation of chemotaxis / semaphorin receptor activity / positive regulation of potassium ion transport / phosphatidylethanolamine binding / positive regulation of proteasomal protein catabolic process / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / cellular response to lipid / kinase activator activity / regulation of interleukin-6 production / apoptotic cell clearance / dendritic spine maintenance / negative regulation of interleukin-1 beta production / phagocytosis, engulfment / regulation of innate immune response / positive regulation of ATP biosynthetic process / phosphatidylserine binding / negative regulation of cholesterol storage / pyroptotic inflammatory response / detection of maltose stimulus / regulation of cytokine production involved in inflammatory response / lipid homeostasis / maltose transport complex / social behavior / cellular response to lipoteichoic acid / amyloid-beta clearance / lipoprotein particle binding / carbohydrate transport / positive regulation of intracellular signal transduction / humoral immune response / regulation of lipid metabolic process / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / apolipoprotein binding / plasma membrane raft / positive regulation of cholesterol efflux / carbohydrate transmembrane transporter activity / maltose binding / positive regulation of TOR signaling
Similarity search - Function
: / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Immunoglobulin V-set domain / D-Maltodextrin-Binding Protein; domain 2 / Immunoglobulin V-set domain ...: / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Immunoglobulin V-set domain / D-Maltodextrin-Binding Protein; domain 2 / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / 2-[(4-bromophenyl)amino]ethan-1-ol / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / Triggering receptor expressed on myeloid cells 2
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.466 Å
AuthorsSu, H.P.
CitationJournal: Protein Expr.Purif. / Year: 2021
Title: Development of a robust crystallization platform for immune receptor TREM2 using a crystallization chaperone strategy.
Authors: Byrne, N.J. / Lee, A.C. / Kostas, J. / Reid, J.C. / Partridge, A.T. / So, S.S. / Cowan, J.E. / Abeywickrema, P. / Huang, H. / Zebisch, M. / Barker, J.J. / Soisson, S.M. / Brooun, A. / Su, H.P.
History
DepositionJun 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1276
Polymers54,1721
Non-polymers9555
Water9,512528
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.840, 80.350, 103.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2 / TREM-2 / Triggering receptor expressed on monocytes 2


Mass: 54172.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea), (gene. exp.) Homo sapiens (human)
Gene: malE, DU74_04045, TREM2 / Production host: Homo sapiens (human)
References: UniProt: A0A0F8NYV9, UniProt: Q9NZC2, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-V5S / 2-[(4-bromophenyl)amino]ethan-1-ol


Mass: 216.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10BrNO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM BisTris pH 5.5, 100 mM ammonium acetate, 15% PEG4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91636 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91636 Å / Relative weight: 1
ReflectionResolution: 1.466→21.44 Å / Num. obs: 76286 / % possible obs: 72.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.74 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 1.466→1.608 Å / Redundancy: 6 % / Num. unique obs: 3814 / CC1/2: 0.572 / % possible all: 15.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACT3.25data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.466→21.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 3827 5.02 %RANDOM
Rwork0.1881 ---
obs0.189 76246 71.7 %-
Displacement parametersBiso max: 74.29 Å2 / Biso mean: 26.14 Å2 / Biso min: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.1416 Å20 Å20 Å2
2--0.1422 Å20 Å2
3----0.0006 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.466→21.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 75 529 4368
Biso mean--27.63 38.74 -
Num. residues----485
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1415SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes726HARMONIC8
X-RAY DIFFRACTIONt_it4057HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion541SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4101SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4083HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5600HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion15.23
LS refinement shellResolution: 1.47→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2223 88 5.77 %
Rwork0.2084 1437 -
all0.2092 1525 -
obs--9.22 %

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