[English] 日本語
Yorodumi
- PDB-2ndh: NMR solution structure of MAL/TIRAP TIR domain (C116A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ndh
TitleNMR solution structure of MAL/TIRAP TIR domain (C116A)
ComponentsToll/interleukin-1 receptor domain-containing adapter protein
KeywordsIMMUNE SYSTEM
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 2 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 4 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 2 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / myeloid cell differentiation / MyD88 deficiency (TLR2/4) / positive regulation of chemokine (C-X-C motif) ligand 2 production / 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 innate immune response / extrinsic component of cytoplasmic side of plasma membrane / cellular response to lipoteichoic acid / endocytic vesicle / signaling adaptor activity / positive regulation of B cell proliferation / 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 / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / 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 / TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
Toll/interleukin-1 receptor domain-containing adapter protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsLavrencic, P. / Mobli, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Solution structure of the TLR adaptor MAL/TIRAP reveals an intact BB loop and supports MAL Cys91 glutathionylation for signaling.
Authors: Hughes, M.M. / Lavrencic, P. / Coll, R.C. / Ve, T. / Ryan, D.G. / Williams, N.C. / Menon, D. / Mansell, A. / Board, P.G. / Mobli, M. / Kobe, B. / O'Neill, L.A.J.
History
DepositionMay 27, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1lowest energy

-
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: 15726.875 Da / Num. of mol.: 1 / Fragment: TIR domain residues 79-221 / Mutation: C116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIRAP, MAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P58753

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR solution structure of the MAL/TIRAP TIR domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D (H)CCH-TOCSY
1612D 1H-13C HSQC aliphatic
1712D 1H-13C HSQC aromatic
1813D 1H-15N NOESY
1913D HBHA(CO)NH
11013D HN(CO)CA

-
Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] protein, 20 mM TRIS, 5 % D2O, 200 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMentity-1[U-99% 13C; U-99% 15N]1
20 mMTRIS-21
5 %D2O-31
200 mMsodium chloride-41
Sample conditionsIonic strength: 0.2 / pH: 8.6 / Pressure: ambient / Temperature: 291 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSTALOS+Cornilescu, Delaglio and Baxchemical shift calculation
CCPNMR2.4CCPNchemical shift assignment
CCPNMR2.4CCPNdata analysis
CCPNMR2.4CCPNpeak picking
TopSpinBruker Biospinprocessing
Rowland_NMR_toolkit3JC Hoch et al.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Automated NOE assignment
NMR constraintsNOE constraints total: 1363 / NOE intraresidue total count: 362 / NOE long range total count: 262 / NOE medium range total count: 317 / NOE sequential total count: 422 / Protein phi angle constraints total count: 106 / Protein psi angle constraints total count: 110
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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