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- PDB-6l9v: Crystal structure of mouse TIFA (T9D/C36S mutant) -

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Basic information

Entry
Database: PDB / ID: 6l9v
TitleCrystal structure of mouse TIFA (T9D/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 / canonical NF-kappaB signal transduction / 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: 3.05 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


Theoretical massNumber of molelcules
Total (without water)90,5984
Polymers90,5984
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)45,2992
Polymers45,2992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-6 kcal/mol
Surface area13820 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)45,2992
Polymers45,2992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.570, 114.570, 167.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 22649.389 Da / Num. of mol.: 4 / Mutation: T9D, 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: Sodium citrate pH 5.3, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.05→47.57 Å / Num. obs: 14468 / % possible obs: 92.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 16
Reflection shellResolution: 3.05→3.13 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 1064

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L9U

6l9u


Resolution: 3.05→47.57 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 15.345 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 731 4.9 %RANDOM
Rwork0.2234 ---
obs0.2244 14082 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 173.31 Å2 / Biso mean: 108.688 Å2 / Biso min: 78.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 3.05→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 0 0 4559
Num. residues----555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0194651
X-RAY DIFFRACTIONr_bond_other_d0.0010.024446
X-RAY DIFFRACTIONr_angle_refined_deg0.6281.9636224
X-RAY DIFFRACTIONr_angle_other_deg0.566310281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.625551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.30124.89227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.52315918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5271520
X-RAY DIFFRACTIONr_chiral_restr0.0450.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025201
X-RAY DIFFRACTIONr_gen_planes_other00.021119
LS refinement shellResolution: 3.05→3.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 47 -
Rwork0.233 1063 -
all-1110 -
obs--96.44 %

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