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- PDB-2m1w: TICAM-2 TIR domain -

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Basic information

Entry
Database: PDB / ID: 2m1w
TitleTICAM-2 TIR domain
ComponentsTIR domain-containing adapter molecule 2
KeywordsIMMUNE SYSTEM / TIR domain / TICAM-2 / TRAM / innate immunity / Interferon
Function / homology
Function and homology information


MyD88-independent toll-like receptor signaling pathway / TRAM-dependent toll-like receptor 4 signaling pathway / positive regulation of interleukin-18-mediated signaling pathway / negative regulation of chemokine (C-C motif) ligand 5 production / negative regulation of MyD88-independent toll-like receptor signaling pathway / neutrophil degranulation / MyD88-independent TLR4 cascade / positive regulation of toll-like receptor 4 signaling pathway / TRIF-mediated programmed cell death / negative regulation of toll-like receptor 4 signaling pathway ...MyD88-independent toll-like receptor signaling pathway / TRAM-dependent toll-like receptor 4 signaling pathway / positive regulation of interleukin-18-mediated signaling pathway / negative regulation of chemokine (C-C motif) ligand 5 production / negative regulation of MyD88-independent toll-like receptor signaling pathway / neutrophil degranulation / MyD88-independent TLR4 cascade / positive regulation of toll-like receptor 4 signaling pathway / TRIF-mediated programmed cell death / negative regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / TRIF-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / COPII-coated ER to Golgi transport vesicle / Golgi organization / necroptotic process / phagocytic cup / endoplasmic reticulum-Golgi intermediate compartment / canonical NF-kappaB signal transduction / endoplasmic reticulum to Golgi vesicle-mediated transport / phagocytosis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / secretory granule membrane / cell projection / apoptotic signaling pathway / intracellular protein transport / late endosome / late endosome membrane / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / early endosome / endosome membrane / inflammatory response / innate immune response / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / plasma membrane
Similarity search - Function
Transmembrane emp24 domain-containing protein / TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
TIR domain-containing adapter molecule 2
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 2


Theoretical massNumber of molelcules
Total (without water)19,3861
Polymers19,3861
Non-polymers00
Water0
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 2 / TICAM-2 / Putative NF-kappa-B-activating protein 502 / TRIF-related adapter molecule / Toll-like ...TICAM-2 / Putative NF-kappa-B-activating protein 502 / TRIF-related adapter molecule / Toll-like receptor adaptor protein 3 / Toll/interleukin-1 receptor domain-containing protein


Mass: 19385.865 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 75-235 / Mutation: H117C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TICAM2, TIRAP3, TIRP, TRAM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86XR7

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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 HBHA(CO)NH
11013D HN(CA)HA
11113D H(CCO)NH
11213D C(CO)NH
11313D (H)CCH-TOCSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5mM [U-99% 13C; U-99% 15N] TICAM-2 TIR-1, 50mM HEPES-NaOH-2, 10mM DTT-3, 5% [U-100% 2H] glycerol-4, 0.02 mg/mL DSS-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTICAM-2 TIR-1[U-99% 13C; U-99% 15N]1
50 mMHEPES-NaOH-21
10 mMDTT-31
5 %glycerol-4[U-100% 2H]1
0.02 mg/mLDSS-51
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 293 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
Sparky3.113Goddardrefinement
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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