[English] 日本語
Yorodumi
- PDB-4lqd: The crystal structures of the Brucella protein TcpB and the TLR a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lqd
TitleThe crystal structures of the Brucella protein TcpB and the TLR adaptor protein TIRAP show structural differences in microbial TIR mimicry
ComponentsToll/interleukin-1 receptor domain-containing adapter protein
KeywordsIMMUNE SYSTEM / Flavodoxin Fold / Toll-like receptor Signaling Adaptor / MyD88
Function / homology
Function and homology information


positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / myeloid cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of neutrophil chemotaxis / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / 3'-UTR-mediated mRNA stabilization / regulation of stress-activated MAPK cascade / regulation of innate immune response / cellular response to lipoteichoic acid / endocytic vesicle / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of B cell proliferation / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / positive regulation of interleukin-8 production / protein kinase C binding / positive regulation of JNK cascade / positive regulation of protein-containing complex assembly / ruffle membrane / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / molecular adaptor activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / innate immune response / cell surface / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Toll-interleukin 1 receptor domain-containing adaptor protein, Tirap / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toll/interleukin-1 receptor domain-containing adapter protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.451 Å
AuthorsSnyder, G.A. / Smith, P. / Jiang, J. / Xiao, T.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structures of the Toll/Interleukin-1 receptor (TIR) domains from the Brucella protein TcpB and host adaptor TIRAP reveal mechanisms of molecular mimicry.
Authors: Snyder, G.A. / Deredge, D. / Waldhuber, A. / Fresquez, T. / Wilkins, D.Z. / Smith, P.T. / Durr, S. / Cirl, C. / Jiang, J. / Jennings, W. / Luchetti, T. / Snyder, N. / Sundberg, E.J. / ...Authors: Snyder, G.A. / Deredge, D. / Waldhuber, A. / Fresquez, T. / Wilkins, D.Z. / Smith, P.T. / Durr, S. / Cirl, C. / Jiang, J. / Jennings, W. / Luchetti, T. / Snyder, N. / Sundberg, E.J. / Wintrode, P. / Miethke, T. / Xiao, T.S.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toll/interleukin-1 receptor domain-containing adapter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0081
Non-polymers921
Water1,06359
1
A: Toll/interleukin-1 receptor domain-containing adapter protein
hetero molecules

A: Toll/interleukin-1 receptor domain-containing adapter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2014
Polymers32,0172
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1770 Å2
ΔGint-15 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.570, 87.570, 80.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Toll/interleukin-1 receptor domain-containing adapter protein / TIR domain-containing adapter protein / Adaptor protein Wyatt / MyD88 adapter-like protein / MyD88-2


Mass: 16008.291 Da / Num. of mol.: 1 / Fragment: TIRAP TIR domain (UNP residues 81-221)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIRAP, MAL / Production host: Escherichia coli (E. coli) / References: UniProt: P58753
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.83 Å3/Da / Density % sol: 74.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 5%MPD,100mM Ches pH 9.0, 100mM NaCl and 24% glycerol cryo, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.45→10.96 Å / Num. obs: 12002 / % possible obs: 99.8 % / Observed criterion σ(I): 3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.451→10.96 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 572 4.77 %random
Rwork0.2073 ---
obs0.2079 11998 99.83 %-
all-12002 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.451→10.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 6 59 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061012
X-RAY DIFFRACTIONf_angle_d0.9781366
X-RAY DIFFRACTIONf_dihedral_angle_d13.426375
X-RAY DIFFRACTIONf_chiral_restr0.034148
X-RAY DIFFRACTIONf_plane_restr0.007175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4505-2.69710.29541410.26872786X-RAY DIFFRACTION100
2.6971-3.08720.23571410.24672803X-RAY DIFFRACTION100
3.0872-3.8890.24051480.20382839X-RAY DIFFRACTION100
3.889-39.16750.17961420.18292998X-RAY DIFFRACTION100

+
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