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- PDB-2m1x: TICAM-1 TIR domain structure -

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Basic information

Entry
Database: PDB / ID: 2m1x
TitleTICAM-1 TIR domain structure
ComponentsTIR domain-containing adapter molecule 1
KeywordsIMMUNE SYSTEM / TIR domain / TICAM-1 / Interferon / TRIF / 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
TIR domain-containing adapter molecule 1 / TRIF, N-terminal / : / TRIF N-terminal domain / RHIM domain / RIP homotypic interaction motif / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...TIR domain-containing adapter molecule 1 / TRIF, N-terminal / : / TRIF N-terminal domain / RHIM domain / RIP homotypic interaction motif / Toll/interleukin-1 receptor homology (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
TIR domain-containing adapter molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsEnokizono, Y. / Kumeta, H. / Funami, K. / Horiuchi, M. / Sarmiento, J. / Yamashita, K. / Standley, D.M. / Matsumoto, M. / Seya, T. / Inagaki, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling.
Authors: Enokizono, Y. / Kumeta, H. / Funami, K. / Horiuchi, M. / Sarmiento, J. / Yamashita, K. / Standley, D.M. / Matsumoto, M. / Seya, T. / Inagaki, F.
History
DepositionDec 7, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.2May 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)19,1331
Polymers19,1331
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 / TIR domain-containing adapter protein inducing IFN-beta


Mass: 19132.691 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 387-545 / Mutation: P434H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TICAM1, PRVTIRB, TRIF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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 HNCA
1613D HN(CO)CA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D H(CCO)NH
11013D HBHA(CO)NH
11113D C(CO)NH
11213D (H)CCH-TOCSY
11313D (H)CCH-COSY
11413D HCACO
11513D 1H-15N NOESY
11613D 1H-13C NOESY aliphatic
11712D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] TICAM-1 TIR-1, 20 mM AcOH Buffer-2, 5 mM DTT-3, 0.02 mg/mL DSS-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTICAM-1 TIR-1[U-99% 13C; U-99% 15N]1
20 mMAcOH Buffer-21
5 mMDTT-31
0.02 mg/mLDSS-41
Sample conditionsIonic strength: 20 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2007.068.09.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddarddata analysis
Sparky3.113Goddardrefinement
TALOS2007.068.09.07Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, 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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