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- PDB-2m63: The protease-resistant N-terminal domain of TIR-domain containing... -

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Basic information

Entry
Database: PDB / ID: 2m63
TitleThe protease-resistant N-terminal domain of TIR-domain containing adaptor molecule-1, TICAM-1
ComponentsTIR domain-containing adapter molecule 1
KeywordsIMMUNE SYSTEM / TICAM-1 / TRIF / Interferon / innate immunity
Function / homology
Function and homology information


TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production ...TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production / Caspase activation via Death Receptors in the presence of ligand / toll-like receptor 3 signaling pathway / TRIF-dependent toll-like receptor signaling pathway / RIP-mediated NFkB activation via ZBP1 / macrophage activation involved in immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / response to exogenous dsRNA / B cell proliferation / regulation of protein-containing complex assembly / autophagosome / positive regulation of type I interferon production / positive regulation of autophagy / signaling adaptor activity / positive regulation of chemokine production / positive regulation of B cell proliferation / lipopolysaccharide-mediated signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / nitric oxide biosynthetic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / apoptotic signaling pathway / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / molecular adaptor activity / early endosome / endosome membrane / endosome / inflammatory response / innate immune response / positive regulation of gene expression / protein kinase binding / mitochondrion / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #780 / TIR domain-containing adapter molecule 1 / TRIF, N-terminal / : / TRIF N-terminal domain / RHIM domain / RIP homotypic interaction motif / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #780 / TIR domain-containing adapter molecule 1 / TRIF, N-terminal / : / TRIF N-terminal domain / RHIM domain / RIP homotypic interaction motif / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
TIR domain-containing adapter molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model1
AuthorsKumeta, H. / Enokizono, Y. / Sakakibara, H. / Ogura, K. / Matsumoto, M. / Seya, T. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2014
Title: The N-terminal domain of TIR domain-containing adaptor molecule-1, TICAM-1.
Authors: Kumeta, H. / Sakakibara, H. / Enokizono, Y. / Ogura, K. / Horiuchi, M. / Matsumoto, M. / Seya, T. / Inagaki, F.
History
DepositionMar 20, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TIR domain-containing adapter molecule 1


Theoretical massNumber of molelcules
Total (without water)17,3991
Polymers17,3991
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein TIR domain-containing adapter molecule 1 / TICAM-1 / Proline-rich / vinculin and TIR domain-containing protein B / Putative NF-kappa-B- ...TICAM-1 / Proline-rich / vinculin and TIR domain-containing protein B / Putative NF-kappa-B-activating protein 502H / Toll-interleukin-1 receptor domain-containing adapter protein inducing interferon beta / MyD88-3 / TIR domain-containing adapter protein inducing IFN-beta


Mass: 17398.713 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TICAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IUC6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HN(CO)CA
1613D HNCA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HN(CA)HA
11113D C(CO)NH
11213D (H)CCH-TOCSY
11313D 1H-15N NOESY
11413D 1H-13C NOESY aliphatic
11513D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.75 mM [U-99% 13C; U-99% 15N] TICAM-1_NTD-1, 3 mM DTT-2, 50 mM sodium phosphate-3, 1 mM sodium azide-4, 0.02 mg/mL DSS-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMTICAM-1_NTD-1[U-99% 13C; U-99% 15N]1
3 mMDTT-21
50 mMsodium phosphate-31
1 mMsodium azide-41
0.02 mg/mLDSS-51
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity INOVAVarianUnity INOVA8001
Varian Unity INOVAVarianUnity INOVA6002

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Processing

NMR software
NameVersionClassification
VNMR6.1Ccollection
CYANArefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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