[English] 日本語
Yorodumi
- PDB-6yye: TREM2 extracellular domain (19-131) in complex with single-chain ... -

+
Open data


ID or keywords:

Loading...

-
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 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 / negative regulation of autophagic cell death / respiratory burst after phagocytosis / negative regulation of astrocyte activation / positive regulation of CAMKK-AMPK signaling cascade / semaphorin receptor binding / positive regulation of low-density lipoprotein particle clearance / positive regulation of microglial cell migration / detection of lipopolysaccharide / apolipoprotein A-I binding / Other semaphorin interactions / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / CXCL12-activated CXCR4 signaling pathway / 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 / dendritic cell differentiation / microglial cell proliferation / positive regulation of microglial cell activation / phagocytosis, recognition / semaphorin receptor complex / amyloid-beta clearance by cellular catabolic process / low-density lipoprotein particle binding / cellular response to lipoprotein particle stimulus / regulation of resting membrane potential / positive regulation of phagocytosis, engulfment / negative regulation of NLRP3 inflammasome complex assembly / regulation of TOR signaling / cellular response to peptidoglycan / peptidoglycan binding / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of chemotaxis / positive regulation of amyloid-beta clearance / positive regulation of potassium ion transport / semaphorin receptor activity / 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 / phosphatidylserine binding / pyroptotic inflammatory response / regulation of cytokine production involved in inflammatory response / negative regulation of cholesterol storage / cellular response to lipoteichoic acid / lipid homeostasis / amyloid-beta clearance / lipoprotein particle binding / positive regulation of ATP biosynthetic process / humoral immune response / positive regulation of intracellular signal transduction / regulation of lipid metabolic process / positive regulation of interleukin-10 production / apolipoprotein binding / plasma membrane raft / negative regulation of tumor necrosis factor production / social behavior / positive regulation of cholesterol efflux / positive regulation of TOR signaling / response to axon injury / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / astrocyte activation / 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 / Immunoglobulins / 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: 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more