[English] 日本語
Yorodumi
- PDB-3wpd: Crystal structure of horse TLR9 in complex with inhibitory DNA4084 -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


positive regulation of intestinal epithelial cell development / cellular response to chloroquine / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / regulation of dendritic cell cytokine production / positive regulation of toll-like receptor 9 signaling pathway / maintenance of gastrointestinal epithelium / positive regulation of interleukin-18 production / positive regulation of B cell activation ...positive regulation of intestinal epithelial cell development / cellular response to chloroquine / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / regulation of dendritic cell cytokine production / positive regulation of toll-like receptor 9 signaling pathway / maintenance of gastrointestinal epithelium / positive regulation of interleukin-18 production / positive regulation of B cell activation / 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 / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / positive regulation of immunoglobulin production / canonical NF-kappaB signal transduction / phagocytic vesicle / positive regulation of B cell proliferation / positive regulation of chemokine production / activation of innate immune response / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein phosphorylation / negative regulation of ERK1 and ERK2 cascade / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / lysosome / inflammatory response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily ...Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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 / Toll-like receptor 9
Similarity search - Component
Biological speciesEquus caballus (horse)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsOhto, U. / Tanji, H. / 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toll-like receptor 9
C: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6848
Polymers92,5292
Non-polymers1,1556
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-13 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.550, 117.080, 69.570
Angle α, β, γ (deg.)90.00, 105.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-903-

SO4

-
Components

-
Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Toll-like receptor 9 /


Mass: 89427.562 Da / Num. of mol.: 1 / Fragment: UNP residues 26-817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: TLR9 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q2EEY0
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3')


Mass: 3101.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

-
Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

-
Non-polymers , 2 types, 13 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 14-10% PEG 3350, 0.2M ammonium sulfate, 0.1M Na acetate pH 4.5, 10% ethylene glycol , 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: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→67.05 Å / Num. obs: 23567 / Rsym value: 0.143

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→58.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 15.539 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25808 1212 5.1 %RANDOM
Rwork0.20062 ---
obs0.20364 22352 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.106 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å2-0 Å2-2.19 Å2
2---3.28 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.75→58.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5909 206 71 10 6196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196342
X-RAY DIFFRACTIONr_bond_other_d0.0010.025995
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9558680
X-RAY DIFFRACTIONr_angle_other_deg0.8423.00213716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2115750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46323.547265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79515999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8691541
X-RAY DIFFRACTIONr_chiral_restr0.0730.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021502
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.753→2.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 98 -
Rwork0.288 1619 -
obs--99.77 %

+
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