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- PDB-8wwy: Crystal structure of mouse TIFA/TIFAB heterodimer -

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Basic information

Entry
Database: PDB / ID: 8wwy
TitleCrystal structure of mouse TIFA/TIFAB heterodimer
Components
  • TRAF-interacting protein with FHA domain-containing protein A
  • TRAF-interacting protein with FHA domain-containing protein B
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


regulation of muscle organ development / learned vocalization behavior / negative regulation of saliva secretion / hard palate morphogenesis / negative regulation of relaxation of muscle / trigeminal nerve development / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / craniofacial suture morphogenesis / thorax and anterior abdomen determination / vestibulocochlear nerve formation ...regulation of muscle organ development / learned vocalization behavior / negative regulation of saliva secretion / hard palate morphogenesis / negative regulation of relaxation of muscle / trigeminal nerve development / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / craniofacial suture morphogenesis / thorax and anterior abdomen determination / vestibulocochlear nerve formation / Alpha-protein kinase 1 signaling pathway / genitalia morphogenesis / TAK1-dependent IKK and NF-kappa-B activation / mastication / peristalsis / cochlea morphogenesis / auditory behavior / myeloid cell differentiation / deubiquitinase activator activity / toll-like receptor signaling pathway / neuromuscular process controlling balance / cytoplasmic pattern recognition receptor signaling pathway / hematopoietic progenitor cell differentiation / lipopolysaccharide-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / protein homooligomerization / regulation of gene expression / 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
(2R,5R)-hexane-2,5-diol / TRAF-interacting protein with FHA domain-containing protein A / TRAF-interacting protein with FHA domain-containing protein B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsNakamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA.
Authors: Nakamura, T. / Ohyama, C. / Sakamoto, M. / Toma, T. / Tateishi, H. / Matsuo, M. / Chirifu, M. / Ikemizu, S. / Morioka, H. / Fujita, M. / Inoue, J.I. / Yamagata, Y.
History
DepositionOct 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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 B
C: TRAF-interacting protein with FHA domain-containing protein A
D: TRAF-interacting protein with FHA domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9638
Polymers67,4904
Non-polymers4734
Water8,557475
1
A: TRAF-interacting protein with FHA domain-containing protein A
B: TRAF-interacting protein with FHA domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8633
Polymers33,7452
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-2 kcal/mol
Surface area13400 Å2
MethodPISA
2
C: TRAF-interacting protein with FHA domain-containing protein A
D: TRAF-interacting protein with FHA domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0995
Polymers33,7452
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-3 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.758, 88.758, 297.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-209-

HOH

21B-330-

HOH

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Components

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


Mass: 17577.070 Da / Num. of mol.: 2 / Mutation: C36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tifa / Production host: Escherichia coli (E. coli) / References: UniProt: Q793I8
#2: Protein TRAF-interacting protein with FHA domain-containing protein B


Mass: 16167.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tifab / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JZM6
#3: Chemical
ChemComp-HX2 / (2R,5R)-hexane-2,5-diol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, PEG 2000, Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→47.04 Å / Num. obs: 65696 / % possible obs: 99.7 % / Redundancy: 19.5 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 1 / Net I/σ(I): 21.4
Reflection shellResolution: 1.79→1.9 Å / Num. unique obs: 10329 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→47.04 Å / SU ML: 0.2006 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3703 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2248 3282 5 %
Rwork0.1811 62397 -
obs0.1833 65679 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.83 Å2
Refinement stepCycle: LAST / Resolution: 1.79→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 32 475 4929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574727
X-RAY DIFFRACTIONf_angle_d0.81826395
X-RAY DIFFRACTIONf_chiral_restr0.0541706
X-RAY DIFFRACTIONf_plane_restr0.0048824
X-RAY DIFFRACTIONf_dihedral_angle_d11.55992891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.820.32121380.29662618X-RAY DIFFRACTION98.5
1.82-1.850.27191410.26572687X-RAY DIFFRACTION99.3
1.85-1.880.28011370.24452607X-RAY DIFFRACTION99.17
1.88-1.910.30431390.2432636X-RAY DIFFRACTION99.32
1.91-1.950.23991400.23532655X-RAY DIFFRACTION99.4
1.95-1.980.26431400.22032662X-RAY DIFFRACTION99.43
1.98-2.030.25251420.20682697X-RAY DIFFRACTION99.54
2.03-2.070.24771390.19712645X-RAY DIFFRACTION99.54
2.07-2.120.25661410.19512672X-RAY DIFFRACTION99.61
2.12-2.170.2421400.18632662X-RAY DIFFRACTION99.47
2.17-2.230.21181420.18412691X-RAY DIFFRACTION99.75
2.23-2.290.24591400.18232671X-RAY DIFFRACTION99.68
2.29-2.370.2611420.19332685X-RAY DIFFRACTION99.79
2.37-2.450.23491410.18512691X-RAY DIFFRACTION99.75
2.45-2.550.23671430.19212712X-RAY DIFFRACTION99.93
2.55-2.670.22821430.19432716X-RAY DIFFRACTION99.97
2.67-2.810.20411430.18712722X-RAY DIFFRACTION99.97
2.81-2.980.25651450.1792746X-RAY DIFFRACTION99.97
2.98-3.210.23881450.18022749X-RAY DIFFRACTION100
3.21-3.540.18961460.1612773X-RAY DIFFRACTION100
3.54-4.050.19051470.15482806X-RAY DIFFRACTION100
4.05-5.10.17331500.13782840X-RAY DIFFRACTION100
5.1-47.040.27121580.21183054X-RAY DIFFRACTION99.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.580188265380.3987912059180.8321085952070.9629162787780.03879188545662.46938423340.04347138098280.1352149413450.123869898177-0.01624454179570.003426169896620.1479812163310.146564455663-0.301582444404-0.02692269723820.183500044369-0.02771330335190.02029916174850.2657993266850.04487416918060.2367649756157.37678615627-26.3194516114-19.747181705
22.018925545410.06905140502730.3442544118231.48316368156-0.5103761263841.88565704473-0.09847243249660.261654240356-0.198974810771-0.1419805419640.07514246265950.04554971044660.230380163482-0.02767788646810.008939251930610.209173407298-0.003698890167550.0158863055160.202515674528-0.05438084397950.22180476434336.0698366948-42.1610124822-23.0576871183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B
2X-RAY DIFFRACTION2chain C or chain D

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