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- PDB-6yye: TREM2 extracellular domain (19-131) in complex with single-chain ... -

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Basic information

Entry
Database: PDB / ID: 6yye
TitleTREM2 extracellular domain (19-131) in complex with single-chain variable fragment (scFv-2)
Components
  • TREM2 Single chain variable 2
  • Triggering receptor expressed on myeloid cells 2
KeywordsIMMUNE SYSTEM / scFv / complex / receptor / Alzheimer's
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 / cellular response to lipid / positive regulation of kinase activity / 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 / negative regulation of cholesterol storage / phosphatidylserine binding / pyroptotic inflammatory response / regulation of cytokine production involved in inflammatory response / lipid homeostasis / plasma membrane raft / lipoprotein particle binding / cellular response to lipoteichoic acid / apolipoprotein binding / social behavior / positive regulation of interleukin-10 production / humoral immune response / negative regulation of tumor necrosis factor production / regulation of lipid metabolic process / positive regulation of TOR signaling / response to axon injury / positive regulation of cholesterol efflux / negative regulation of cytokine production involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Immunoglobulin-like fold
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: 3.36 Å
AuthorsSzykowska, A. / Preger, C. / Krojer, T. / Mukhopadhyay, S.M.M. / McKinley, G. / Graslund, S. / Wigren, E. / Persson, H. / von Delft, F. / Arrowsmith, C.H. ...Szykowska, A. / Preger, C. / Krojer, T. / Mukhopadhyay, S.M.M. / McKinley, G. / Graslund, S. / Wigren, E. / Persson, H. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Di Daniel, E. / Burgess-Brown, N. / Bullock, A.
Citation
Journal: Structure / Year: 2021
Title: Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain.
Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S.M. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / ...Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S.M. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / Mead, E. / Wang, J. / Davis, J.B. / Burgess-Brown, N.A. / Bullock, A.N.
#1: Journal: Biorxiv / Year: 2021
Title: Selection and structural characterisation of anti-TREM2 scFvs that reduce levels of shed ectodomain
Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / Mead, ...Authors: Szykowska, A. / Chen, Y. / Smith, T.B. / Preger, C. / Yang, J. / Qian, D. / Mukhopadhyay, S. / Wigren, E. / Neame, S.J. / Graslund, S. / Persson, H. / Atkinson, P.J. / Di Daniel, E. / Mead, E. / Wang, J. / Davis, J.B. / Burgess-Brown, N.A. / Bullock, A.N.
History
DepositionMay 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Nov 17, 2021Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_ISSN / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: TREM2 Single chain variable 2
D: TREM2 Single chain variable 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5265
Polymers78,3054
Non-polymers2211
Water00
1
A: Triggering receptor expressed on myeloid cells 2
C: TREM2 Single chain variable 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3743
Polymers39,1532
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-6 kcal/mol
Surface area15380 Å2
MethodPISA
2
B: Triggering receptor expressed on myeloid cells 2
D: TREM2 Single chain variable 2


Theoretical massNumber of molelcules
Total (without water)39,1532
Polymers39,1532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.942, 126.201, 225.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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Components

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


Mass: 12951.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLAD
Source: (gene. exp.) Homo sapiens (human) / Gene: TREM2 / Production host: Homo sapiens (human) / References: UniProt: Q9NZC2
#2: Antibody TREM2 Single chain variable 2


Mass: 26200.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: 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.: 1
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
Has ligand of interestN

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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: 5.39 Å3/Da / Density % sol: 77.18 % / Description: Large cubes
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.015M nickel chloride,0.1M tris pH 8.5,2.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9763 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.356→110.07 Å / Num. obs: 16278 / % possible obs: 92 % / Redundancy: 13.4 % / Biso Wilson estimate: 79.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.4
Reflection shellResolution: 3.356→3.679 Å / Num. unique obs: 814 / CC1/2: 0.749

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CY6

6cy6


Resolution: 3.36→110.07 Å / SU ML: 0.5925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3272 774 4.76 %RANDOM
Rwork0.2985 15498 --
obs0.2998 16272 68.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.39 Å2
Refinement stepCycle: LAST / Resolution: 3.36→110.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 0 0 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255166
X-RAY DIFFRACTIONf_angle_d0.53497037
X-RAY DIFFRACTIONf_chiral_restr0.0412785
X-RAY DIFFRACTIONf_plane_restr0.0046901
X-RAY DIFFRACTIONf_dihedral_angle_d12.841736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.570.4107150.401353X-RAY DIFFRACTION9.52
3.57-3.840.4053690.37761283X-RAY DIFFRACTION34.91
3.84-4.230.36061230.34892497X-RAY DIFFRACTION67.2
4.23-4.840.31281880.29313708X-RAY DIFFRACTION99.51
4.84-6.10.3241960.27963747X-RAY DIFFRACTION99.92
6.1-112.50.31111830.28283910X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: -26.1951235583 Å / Origin y: -30.813459225 Å / Origin z: -57.1322426139 Å
111213212223313233
T0.94777828888 Å2-0.214287690373 Å2-0.192996499363 Å2-0.551034362607 Å2-0.0617815723679 Å2--0.618157093051 Å2
L2.03421105211 °2-1.22036364236 °2-1.41485375453 °2-1.4748200899 °21.81245131606 °2--3.88232190562 °2
S0.420569709283 Å °-0.113943205194 Å °0.193546547826 Å °0.100758581013 Å °0.13751364083 Å °-0.35484438665 Å °0.410746938808 Å °-0.0261036113068 Å °-0.490077514215 Å °
Refinement TLS groupSelection details: all

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