[English] 日本語
Yorodumi
- PDB-4om7: Crystal structure of TIR domain of TLR6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4om7
TitleCrystal structure of TIR domain of TLR6
ComponentsToll-like receptor 6
KeywordsSIGNALING PROTEIN / TIR fold / Protein interaction
Function / homology
Function and homology information


toll-like receptor 6 signaling pathway / regulation of cytokine production => GO:0001817 / interleukin-1 beta production / : / toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / cellular response to bacterial lipopeptide ...toll-like receptor 6 signaling pathway / regulation of cytokine production => GO:0001817 / interleukin-1 beta production / : / toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / negative regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / NADP+ nucleosidase activity / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of interleukin-8 production / cell activation / Regulation of TLR by endogenous ligand / lipopeptide binding / TRIF-dependent toll-like receptor signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / activation of NF-kappaB-inducing kinase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage activation / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / nitric oxide metabolic process / plasma membrane => GO:0005886 / positive regulation of JUN kinase activity / microglial cell activation / cellular response to amyloid-beta / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / receptor complex / defense response to bacterium / inflammatory response / immune response / membrane raft / protein heterodimerization activity / innate immune response / signaling receptor binding / positive regulation of gene expression / Golgi apparatus / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Toll-like receptor 6 / Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Toll-like receptor 6 / Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsPark, H.H. / Jang, T.H.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal Structure of TIR Domain of TLR6 Reveals Novel Dimeric Interface of TIR-TIR Interaction for Toll-Like Receptor Signaling Pathway.
Authors: Jang, T.H. / Park, H.H.
History
DepositionJan 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toll-like receptor 6
B: Toll-like receptor 6


Theoretical massNumber of molelcules
Total (without water)42,4212
Polymers42,4212
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.607, 44.199, 75.723
Angle α, β, γ (deg.)90.00, 118.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-910-

HOH

-
Components

#1: Protein Toll-like receptor 6


Mass: 21210.295 Da / Num. of mol.: 2 / Fragment: UNP residues 640-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.2M lithium sulfate monohydrate, 0.1M Tris pH 8.6, 25%(w/v) polyethylene glycol 3350 and 4%(v/v) formamide, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 18245 / % possible obs: 14 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4
Reflection shellResolution: 2.2→2.4 Å / % possible all: 92

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→31.822 Å / SU ML: 0.32 / σ(F): 0.6 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 944 5.18 %random
Rwork0.2334 ---
obs0.236 18212 96.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→31.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 0 27 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092483
X-RAY DIFFRACTIONf_angle_d1.393362
X-RAY DIFFRACTIONf_dihedral_angle_d14.909904
X-RAY DIFFRACTIONf_chiral_restr0.092352
X-RAY DIFFRACTIONf_plane_restr0.008424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.204-2.320.35151200.30712461X-RAY DIFFRACTION96
2.32-2.46530.30941350.29492451X-RAY DIFFRACTION97
2.4653-2.65560.31141410.27222471X-RAY DIFFRACTION97
2.6556-2.92260.3261450.26172510X-RAY DIFFRACTION98
2.9226-3.34520.28841500.24992485X-RAY DIFFRACTION98
3.3452-4.2130.2641400.21342482X-RAY DIFFRACTION96
4.213-31.82550.27481130.21422408X-RAY DIFFRACTION90

+
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