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- PDB-6l9w: Crystal structure of mouse TIFA (T9E/C36S mutant) -

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Basic information

Entry
Database: PDB / ID: 6l9w
TitleCrystal structure of mouse TIFA (T9E/C36S mutant)
ComponentsTRAF-interacting protein with FHA domain-containing protein A
KeywordsSIGNALING PROTEIN / FHA domain
Function / homology
Function and homology information


Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / cytoplasmic pattern recognition receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / protein homooligomerization / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cytoplasm
Similarity search - Function
TRAF-interacting protein with FHA domain-containing protein / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
TRAF-interacting protein with FHA domain-containing protein A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNakamura, T. / Yamagata, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Citation
Journal: Sci Rep / Year: 2020
Title: Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity.
Authors: Nakamura, T. / Hashikawa, C. / Okabe, K. / Yokote, Y. / Chirifu, M. / Toma-Fukai, S. / Nakamura, N. / Matsuo, M. / Kamikariya, M. / Okamoto, Y. / Gohda, J. / Akiyama, T. / Semba, K. / ...Authors: Nakamura, T. / Hashikawa, C. / Okabe, K. / Yokote, Y. / Chirifu, M. / Toma-Fukai, S. / Nakamura, N. / Matsuo, M. / Kamikariya, M. / Okamoto, Y. / Gohda, J. / Akiyama, T. / Semba, K. / Ikemizu, S. / Otsuka, M. / Inoue, J.I. / Yamagata, Y.
#1: Journal: To Be Published
Title: Crystallization and preliminary X-ray analysis of mouse TIFA
Authors: Nakamura, T. / Inoue, J. / Yamagata, Y.
History
DepositionNov 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAF-interacting protein with FHA domain-containing protein A
B: TRAF-interacting protein with FHA domain-containing protein A
C: TRAF-interacting protein with FHA domain-containing protein A
D: TRAF-interacting protein with FHA domain-containing protein A
E: TRAF-interacting protein with FHA domain-containing protein A
F: TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)135,9806
Polymers135,9806
Non-polymers00
Water00
1
A: TRAF-interacting protein with FHA domain-containing protein A
B: TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)45,3272
Polymers45,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-7 kcal/mol
Surface area13330 Å2
MethodPISA
2
C: TRAF-interacting protein with FHA domain-containing protein A
D: TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)45,3272
Polymers45,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-7 kcal/mol
Surface area14140 Å2
MethodPISA
3
E: TRAF-interacting protein with FHA domain-containing protein A
F: TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)45,3272
Polymers45,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-6 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.278, 115.885, 80.938
Angle α, β, γ (deg.)90.000, 106.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TRAF-interacting protein with FHA domain-containing protein A / TRAF2-binding protein


Mass: 22663.414 Da / Num. of mol.: 6 / Mutation: T9E,C36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tifa, T2bp / Production host: Escherichia coli (E. coli) / References: UniProt: Q793I8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: MES pH 6.4, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→37.29 Å / Num. obs: 28175 / % possible obs: 95.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 23.3
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.294 / Num. unique obs: 2170

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L9U

6l9u


Resolution: 2.9→37.29 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.79
RfactorNum. reflection% reflection
Rfree0.2664 1427 5.07 %
Rwork0.2127 --
obs0.2155 28124 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.62 Å2 / Biso mean: 61.7854 Å2 / Biso min: 17.11 Å2
Refinement stepCycle: final / Resolution: 2.9→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6872 0 0 0 6872
Num. residues----837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.99750.45161230.3427200672
2.9975-3.11750.33381330.2752241087
3.1175-3.25930.37811610.244263496
3.2593-3.4310.28871280.2461279399
3.431-3.64580.29321750.25062776100
3.6458-3.9270.25651570.21092781100
3.927-4.32170.25231190.20012802100
4.3217-4.94580.2331490.16352817100
4.9458-6.22640.24761470.20012821100
6.2264-37.290.19761350.19372857100

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