[English] 日本語
Yorodumi
- PDB-6b8o: WT Ig-like V Domain with Phosphatidylserine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b8o
TitleWT Ig-like V Domain with Phosphatidylserine
ComponentsTriggering receptor expressed on myeloid cells 2
KeywordsSIGNALING PROTEIN / Membrane receptor
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 sequestering of triglyceride / 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 / negative regulation of NLRP3 inflammasome complex assembly / microglial cell proliferation / dendritic cell differentiation / complement-mediated synapse pruning / positive regulation of microglial cell activation / regulation of TOR signaling / low-density lipoprotein particle binding / 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 / negative regulation of cholesterol storage / positive regulation of amyloid-beta clearance / phosphatidylethanolamine binding / kinase activator activity / lipid homeostasis / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / positive regulation of kinase activity / cellular response to lipid / apoptotic cell clearance / regulation of interleukin-6 production / negative regulation of interleukin-1 beta production / dendritic spine maintenance / positive regulation of cholesterol efflux / positive regulation of ATP biosynthetic process / phagocytosis, engulfment / regulation of innate immune response / phosphatidylserine binding / pyroptotic inflammatory response / regulation of cytokine production involved in inflammatory response / plasma membrane raft / lipoprotein particle binding / regulation of peptidyl-tyrosine phosphorylation / cellular response to lipoteichoic acid / apolipoprotein binding / positive regulation of interleukin-10 production / social behavior / humoral immune response / negative regulation of tumor necrosis factor production / regulation of lipid metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to axon injury / negative regulation of cytokine production involved in inflammatory response / positive regulation of TOR signaling / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / negative regulation of inflammatory response to antigenic stimulus / positive regulation of calcium-mediated signaling / astrocyte activation / positive regulation of protein localization to plasma membrane
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
IODIDE ION / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Triggering receptor expressed on myeloid cells 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSudom, A. / Wang, Z.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Structure of Ig-like V domain in complex with phosphatidylserine to 2.2 Angstrom resolution
Authors: Sudom, A. / Wang, Z. / Min, X.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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: Triggering receptor expressed on myeloid cells 2
D: Triggering receptor expressed on myeloid cells 2
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)120,08943
Polymers114,8306
Non-polymers5,25937
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15030 Å2
ΔGint-129 kcal/mol
Surface area30400 Å2
Unit cell
Length a, b, c (Å)160.331, 160.331, 86.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein / Sugars , 2 types, 12 molecules ABCDEF

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


Mass: 19138.254 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREM2 / Production host: Homo sapiens (human) / References: UniProt: Q9NZC2
#2: 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.: 6
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

-
Non-polymers , 5 types, 113 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE


Mass: 455.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34NO10P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaI, 1.6 M ammonium sulfate, 50 mM Tris 8.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.2→47.36 Å / Num. obs: 57469 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.8 / Num. measured all: 752391 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.2-2.2613.41.7335914644020.5791.8100
9.59-47.3610.30.034828480716499.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UD7

5ud7


Resolution: 2.2→47.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.77 / SU ML: 0.142 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.184
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 2768 4.8 %RANDOM
Rwork0.2217 ---
obs0.2236 54638 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.23 Å2 / Biso mean: 52.028 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 2.2→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 276 82 5416
Biso mean--73.85 43.78 -
Num. residues----643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195418
X-RAY DIFFRACTIONr_bond_other_d0.0020.024952
X-RAY DIFFRACTIONr_angle_refined_deg2.1651.9767339
X-RAY DIFFRACTIONr_angle_other_deg1.062311439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82622.727231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56615865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3091548
X-RAY DIFFRACTIONr_chiral_restr0.1160.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021117
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 215 -
Rwork0.307 3947 -
all-4162 -
obs--99.98 %

+
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://pdbjlvh1.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