[English] 日本語
Yorodumi
- PDB-5eli: Triggering receptor expressed on myeloid cells 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eli
TitleTriggering receptor expressed on myeloid cells 2
ComponentsTriggering receptor expressed on myeloid cells 2
KeywordsIMMUNE SYSTEM / Activating receptors / TREM2 / innate immunity / immune system 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 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 / 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 / negative regulation of tumor necrosis factor production / apolipoprotein binding / 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 / 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: 3.0977 Å
AuthorsBrett, T.J. / Kober, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL119813 United States
CitationJournal: Elife / Year: 2016
Title: Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms.
Authors: Kober, D.L. / Alexander-Brett, J.M. / Karch, C.M. / Cruchaga, C. / Colonna, M. / Holtzman, M.J. / Brett, T.J.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 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 1.6Sep 27, 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7404
Polymers28,2982
Non-polymers4422
Water00
1
A: Triggering receptor expressed on myeloid cells 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3702
Polymers14,1491
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Triggering receptor expressed on myeloid cells 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3702
Polymers14,1491
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.763, 125.763, 183.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsMonomer confirmed by size exclusion chromatography

-
Components

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


Mass: 14148.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREM2 / Plasmid: pHLSEC / Cell (production host): epithelial / Cell line (production host): HEK293F / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney / 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.: 2
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 protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 7.41 Å3/Da / Density % sol: 85.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 2 M NaCl, 0.2 M MgCl2, 0.2 M NDSB 201, 100 mM HEPES pH 7.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012
RadiationMonochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE CRYSTAL SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.0977→50 Å / Num. all: 16285 / Num. obs: 16285 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 86.38 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 20.96
Reflection shellResolution: 3.0977→3.21 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.72 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9K

1u9k


Resolution: 3.0977→40.689 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 807 4.99 %Random selection
Rwork0.2605 ---
obs0.2611 16171 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.86 Å2
Refinement stepCycle: LAST / Resolution: 3.0977→40.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 0 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061826
X-RAY DIFFRACTIONf_angle_d1.1812484
X-RAY DIFFRACTIONf_dihedral_angle_d14.6391076
X-RAY DIFFRACTIONf_chiral_restr0.059284
X-RAY DIFFRACTIONf_plane_restr0.004314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0977-3.29170.40591310.37452482X-RAY DIFFRACTION100
3.2917-3.54580.34511300.30732505X-RAY DIFFRACTION100
3.5458-3.90230.27751320.29522529X-RAY DIFFRACTION100
3.9023-4.46640.26551340.25822532X-RAY DIFFRACTION100
4.4664-5.62480.21711350.21952576X-RAY DIFFRACTION100
5.6248-40.69210.26591450.24222740X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.34763.03784.81634.6598-0.3682.0694-0.06290.9989-0.103-0.97280.3946-1.3782-0.9191.7022-0.3540.94750.05830.25371.13750.11690.8778-42.627314.2105-20.4624
29.1589-1.0821.83836.9655-0.73749.45320.6773-0.14670.9355-0.5209-0.2297-0.3936-1.39440.81160.18061.1101-0.15610.03170.50070.0190.7011-51.599517.4805-6.1158
32.0012-2.71444.14811.0513-0.17258.7695-1.082.0792.7319-0.4493-0.4643-0.75161.98792.18281.74261.4628-0.10270.41371.59220.47272.0853-49.515132.9817-19.1605
45.55212.8751-1.79845.4004-0.29432.08780.21350.34951.11710.3103-0.14560.4974-1.4646-0.54180.02611.15440.0660.07030.48880.0950.6706-59.127913.0733-9.9706
55.79042.0204-0.98875.43823.45193.42020.17770.38890.2857-0.5002-0.6018-0.4902-0.21190.20390.09810.95160.05660.09270.50890.11020.4984-53.216910.6045-13.8902
64.09611.90280.43622.94721.07932.82120.43020.61060.8909-1.79990.14770.1832-1.68380.7318-0.5621.5716-0.02580.23070.94170.23360.8093-51.387819.4832-19.2155
73.16382.25513.37028.06542.42433.49420.77880.86930.7364-0.64470.3578-1.1224-1.58660.8421-0.96121.0755-0.22270.20941.21220.18490.7196-44.977520.1225-18.3546
86.2477-2.0708-2.42281.99884.7827.05030.4808-0.0610.58371.45490.5584-1.14991.89413.1512-1.07791.04450.2492-0.07011.5618-0.50651.0705-67.622627.0636-25.7941
91.2475-0.53941.91787.9369-6.00087.50540.14050.1986-0.1056-0.0562-0.2271-0.4740.14710.36580.07461.01150.3919-0.02930.705-0.00380.5905-70.130512.0165-19.1175
107.4178-1.9208-0.53588.4268-4.914.24060.70750.18040.5831-0.4578-0.72041.7613-1.1861-1.3855-0.13671.19850.4554-0.19151.1618-0.08780.7557-81.044315.4114-23.5929
119.5806-2.21371.48728.09582.05641.30020.2577-0.31-0.0597-0.59580.1469-0.31321.07520.6112-0.75431.08620.1413-0.25950.5668-0.07510.5581-71.28891.0002-22.9352
123.3239-0.1985-0.39624.3855-3.20855.18370.70221.1021-0.0745-1.2966-0.30860.29250.5652-0.5094-0.19371.41230.5258-0.08671.0073-0.00360.5878-71.501612.8413-29.5424
133.4944-0.19930.11064.2529-2.87895.10120.31080.45780.4419-0.0451-0.20180.3405-0.4349-1.4223-0.63381.19920.3527-0.0720.75360.06450.6933-79.600715.9003-19.5743
143.469-0.68530.9235.32684.12596.02990.675-0.2819-0.20311.083-0.3148-0.7181-2.54530.0768-0.02731.33790.4902-0.15170.7668-0.04480.6597-73.505322.4653-24.6848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 116 )
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 131 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 47 )
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 69 )
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 76 )
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 105 )
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 116 )
14X-RAY DIFFRACTION14chain 'B' and (resid 117 through 131 )

+
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