[English] 日本語
Yorodumi
- PDB-3ub2: TIR domain of Mal/TIRAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ub2
TitleTIR domain of Mal/TIRAP
ComponentsToll/interleukin-1 receptor domain-containing adapter protein
KeywordsIMMUNE SYSTEM / TIR domain / TLRs adaptor
Function / homology
Function and homology information


positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / cellular response to bacterial lipopeptide / regulation of interferon-beta production / 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 chemokine (C-X-C motif) ligand 1 production / positive regulation of toll-like receptor 4 signaling pathway ...positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / cellular response to bacterial lipopeptide / regulation of interferon-beta production / 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 chemokine (C-X-C motif) ligand 1 production / positive regulation of toll-like receptor 4 signaling pathway / myeloid cell differentiation / MyD88 deficiency (TLR2/4) / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / IRAK4 deficiency (TLR2/4) / extrinsic component of cytoplasmic side of plasma membrane / 3'-UTR-mediated mRNA stabilization / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / regulation of innate immune response / cellular response to lipoteichoic acid / endocytic vesicle / positive regulation of B cell proliferation / signaling adaptor activity / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / protein kinase C binding / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of protein-containing complex assembly / positive regulation of interleukin-6 production / ruffle membrane / positive regulation of tumor necrosis factor production / ER-Phagosome pathway / protein-macromolecule adaptor activity / response to lipopolysaccharide / molecular adaptor activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-positive bacterium / inflammatory response / innate immune response / cell surface / identical protein binding / plasma membrane / cytoplasm / cytosol
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Toll/interleukin-1 receptor domain-containing adapter protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsShen, Y. / Lin, Z.
CitationJournal: Plos One / Year: 2012
Title: Structural Insights into TIR Domain Specificity of the Bridging Adaptor Mal in TLR4 Signaling
Authors: Lin, Z. / Lu, J. / Zhou, W. / Shen, Y.
History
DepositionOct 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)16,1242
Polymers15,9701
Non-polymers1541
Water19811
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)32,2494
Polymers31,9402
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2140 Å2
ΔGint-22 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.508, 87.508, 81.684
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 / Mal / TIR domain-containing adapter protein / Adaptor protein Wyatt / MyD88 adapter-like protein


Mass: 15970.159 Da / Num. of mol.: 1 / Fragment: TIR domain, UNP residues 78-221
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-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M CHES, 12-20% Glycerol, 150-300mM sodium chloride, 10mM DTT, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12504 / % possible obs: 87.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 55 Å2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 80

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→39.14 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1011124.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 622 5 %RANDOM
Rwork0.248 ---
all0.249 12504 --
obs0.248 12455 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.23 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 61.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.32 Å20 Å20 Å2
2---7.32 Å20 Å2
3---14.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 8 11 990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 86 5 %
Rwork0.335 1646 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6dtt.paramdtt.top

+
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