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- PDB-8t59: Crystal structure of Para.09 bound to TREM2 -

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Basic information

Entry
Database: PDB / ID: 8t59
TitleCrystal structure of Para.09 bound to TREM2
Components
  • Para.09 heavy chain
  • Para.09 light chain
  • Triggering receptor expressed on myeloid cells 2
KeywordsIMMUNE SYSTEM/PEPTIDE BINDING PROTEIN / Antibody / fab / complex / antigen / PEPTIDE BINDING PROTEIN / IMMUNE SYSTEM-PEPTIDE BINDING PROTEIN complex
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 / very-low-density lipoprotein particle binding / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of glial cell apoptotic process / complement-mediated synapse pruning / microglial cell proliferation / dendritic cell differentiation / 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 / dendritic spine maintenance / apoptotic cell clearance / 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 / regulation of cytokine production involved in inflammatory response / lipid homeostasis / social behavior / cellular response to lipoteichoic acid / amyloid-beta clearance / lipoprotein particle binding / positive regulation of intracellular signal transduction / humoral immune response / regulation of lipid metabolic process / positive regulation of interleukin-10 production / apolipoprotein binding / negative regulation of tumor necrosis factor production / plasma membrane raft / positive regulation of cholesterol efflux / positive regulation of TOR signaling / response to axon injury / positive regulation of phagocytosis / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Triggering receptor expressed on myeloid cells 2
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWallweber, H. / Hsu, P.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2024
Title: Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining.
Authors: Hsiao, Y.C. / Wallweber, H.A. / Alberstein, R.G. / Lin, Z. / Du, C. / Etxeberria, A. / Aung, T. / Shang, Y. / Seshasayee, D. / Seeger, F. / Watkins, A.M. / Hansen, D.V. / Bohlen, C.J. / Hsu, P.L. / Hotzel, I.
History
DepositionJun 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Para.09 heavy chain
B: Para.09 light chain
C: Para.09 heavy chain
D: Para.09 light chain
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)101,86324
Polymers100,3786
Non-polymers1,48518
Water10,305572
1
A: Para.09 heavy chain
B: Para.09 light chain
E: Triggering receptor expressed on myeloid cells 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,00313
Polymers50,1893
Non-polymers81410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-121 kcal/mol
Surface area20110 Å2
MethodPISA
2
C: Para.09 heavy chain
D: Para.09 light chain
F: Triggering receptor expressed on myeloid cells 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,86011
Polymers50,1893
Non-polymers6718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-127 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.170, 68.160, 254.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 2 molecules EF

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


Mass: 2145.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NZC2

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Para.09 heavy chain


Mass: 24068.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Para.09 light chain


Mass: 23974.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 590 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH6.0, 10 mM ZnCl2, 20% PEG6000, 3% 1,6-hexandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→33.78 Å / Num. obs: 64863 / % possible obs: 99.88 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 13.08
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 6409 / CC1/2: 0.536

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.78 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 3217 4.96 %
Rwork0.1996 --
obs0.2015 64857 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6813 0 74 572 7459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067097
X-RAY DIFFRACTIONf_angle_d0.9239652
X-RAY DIFFRACTIONf_dihedral_angle_d16.7722551
X-RAY DIFFRACTIONf_chiral_restr0.0551097
X-RAY DIFFRACTIONf_plane_restr0.0071222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.35511500.29972607X-RAY DIFFRACTION100
2.03-2.060.32341340.27382656X-RAY DIFFRACTION100
2.06-2.10.30941240.25272653X-RAY DIFFRACTION100
2.1-2.130.26961440.25162640X-RAY DIFFRACTION100
2.13-2.170.31351340.24032658X-RAY DIFFRACTION100
2.17-2.210.31211360.23832612X-RAY DIFFRACTION100
2.21-2.260.28731540.23462671X-RAY DIFFRACTION100
2.26-2.310.28181370.22592614X-RAY DIFFRACTION100
2.31-2.360.28621320.23432701X-RAY DIFFRACTION100
2.36-2.420.28431450.22392624X-RAY DIFFRACTION100
2.42-2.480.3321350.21962655X-RAY DIFFRACTION100
2.48-2.560.28331410.2152669X-RAY DIFFRACTION100
2.56-2.640.26941300.21742674X-RAY DIFFRACTION100
2.64-2.730.26521520.20942660X-RAY DIFFRACTION100
2.73-2.840.22421290.21122698X-RAY DIFFRACTION100
2.84-2.970.27131610.21852625X-RAY DIFFRACTION100
2.97-3.130.29481330.20742702X-RAY DIFFRACTION100
3.13-3.330.25371110.2062704X-RAY DIFFRACTION100
3.33-3.580.22831450.18662705X-RAY DIFFRACTION100
3.58-3.940.17131370.1742720X-RAY DIFFRACTION100
3.94-4.510.17131520.1562721X-RAY DIFFRACTION99
4.51-5.680.19141500.15942751X-RAY DIFFRACTION100
5.68-33.780.22221510.20542920X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.4338 Å / Origin y: -13.6867 Å / Origin z: -32.7594 Å
111213212223313233
T0.1863 Å2-0.0001 Å2-0 Å2-0.2418 Å2-0.0144 Å2--0.2461 Å2
L0.0656 °20.0076 °2-0.097 °2-0.2228 °2-0.0284 °2--0.5187 °2
S0.0155 Å °0.0018 Å °0.0002 Å °0.059 Å °-0.0207 Å °-0.0066 Å °-0.0439 Å °0.032 Å °0.0077 Å °
Refinement TLS groupSelection details: all

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