[English] 日本語
Yorodumi
- PDB-3wpg: Crystal structure of mouse TLR9 in complex with inhibitory DNA408... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wpg
TitleCrystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 1)
Components
  • DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3')
  • Toll-like receptor 9
KeywordsDNA BINDING PROTEIN/DNA / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / CpG motif / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / cellular response to chloroquine / positive regulation of intestinal epithelial cell development / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / cellular response to metal ion ...Toll Like Receptor 9 (TLR9) Cascade / cellular response to chloroquine / positive regulation of intestinal epithelial cell development / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / cellular response to metal ion / positive regulation of toll-like receptor 9 signaling pathway / regulation of dendritic cell cytokine production / maintenance of gastrointestinal epithelium / positive regulation of B cell activation / positive regulation of interleukin-18 production / unmethylated CpG binding / toll-like receptor 9 signaling pathway / siRNA binding / early phagosome / interleukin-1 receptor binding / positive regulation of granulocyte macrophage colony-stimulating factor production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of immunoglobulin production / pattern recognition receptor activity / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / canonical NF-kappaB signal transduction / positive regulation of chemokine production / phagocytic vesicle / positive regulation of autophagy / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of cytokine production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / response to molecule of bacterial origin / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of ERK1 and ERK2 cascade / response to virus / positive regulation of interleukin-6 production / positive regulation of type II interferon production / male gonad development / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / regulation of inflammatory response / early endosome membrane / defense response to Gram-negative bacterium / basolateral plasma membrane / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of MAPK cascade / endosome / immune response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain ...Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Toll-like receptor 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.246 Å
AuthorsOhto, U. / Shimizu, T.
CitationJournal: Nature / Year: 2015
Title: Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Authors: Ohto, U. / Shibata, T. / Tanji, H. / Ishida, H. / Krayukhina, E. / Uchiyama, S. / Miyake, K. / Shimizu, T.
History
DepositionJan 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / ndb_struct_conf_na / pdbx_chem_comp_identifier / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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: Toll-like receptor 9
B: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6028
Polymers93,9002
Non-polymers7026
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-63 kcal/mol
Surface area31300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.230, 123.860, 130.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Toll-like receptor 9


Mass: 90172.562 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 26-818 / Mutation: N200Q, N242Q, N309Q, N495Q, N568Q, N695Q, N752Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr9 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9EQU3
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3')


Mass: 3727.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 6-8% PEG 8000, 0.4M ammonium sulfate, 0.1M Tris pH 8.0, 10% DMSO , VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.246→55.94 Å / Num. obs: 55799 / Biso Wilson estimate: 39.13 Å2 / Rsym value: 0.12

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.246→35.615 Å / FOM work R set: 0.6952 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 35.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 2823 5.07 %
Rwork0.2359 --
obs0.2382 55710 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.78 Å2 / Biso mean: 57.29 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: LAST / Resolution: 2.246→35.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 227 39 77 6100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046206
X-RAY DIFFRACTIONf_angle_d0.8888452
X-RAY DIFFRACTIONf_chiral_restr0.061985
X-RAY DIFFRACTIONf_plane_restr0.0031027
X-RAY DIFFRACTIONf_dihedral_angle_d16.3022275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.246-2.28470.42591480.39282555270399
2.2847-2.32630.39181370.375526302767100
2.3263-2.3710.41691420.360226072749100
2.371-2.41940.40791350.340626052740100
2.4194-2.4720.37671440.319726212765100
2.472-2.52950.35381240.299426212745100
2.5295-2.59270.35661290.289226182747100
2.5927-2.66280.32451590.278526132772100
2.6628-2.74110.28541490.276126192768100
2.7411-2.82950.3061430.265626192762100
2.8295-2.93060.3671390.274226272766100
2.9306-3.04790.30651300.271226472777100
3.0479-3.18650.31591450.254426302775100
3.1865-3.35440.26391290.243626602789100
3.3544-3.56440.27121480.218426582806100
3.5644-3.83930.26011490.18826442793100
3.8393-4.22510.2481240.182326912815100
4.2251-4.83520.17561270.176927072834100
4.8352-6.08690.23941550.197827002855100
6.0869-35.61950.26021670.23442815298299
Refinement TLS params.Method: refined / Origin x: -2.9957 Å / Origin y: 4.8483 Å / Origin z: -25.3832 Å
111213212223313233
T0.2644 Å2-0.0414 Å20.0341 Å2--0.0046 Å20.0585 Å2--0.2995 Å2
L1.6389 °20.0283 °20.9177 °2-0.2309 °20.1224 °2--3.7257 °2
S-0.0441 Å °0.0916 Å °0.0571 Å °0.0233 Å °0.0593 Å °0.0049 Å °-0.1611 Å °-0.1384 Å °-0.0139 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