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- PDB-4zgi: Structure of Truncated Human TIFA -

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Basic information

Entry
Database: PDB / ID: 4zgi
TitleStructure of Truncated Human TIFA
ComponentsTRAF-interacting protein with FHA domain-containing protein A
KeywordsSIGNALING PROTEIN / FHA domian / adaptor
Function / homology
Function and homology information


cytoplasmic pattern recognition receptor signaling pathway / canonical NF-kappaB signal transduction / Alpha-protein kinase 1 signaling pathway / tumor necrosis factor-mediated signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / protein homooligomerization / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.701 Å
AuthorsWeng, J.H. / Wei, T.Y.W. / Hsieh, Y.C. / Huang, C.C.F. / Wu, P.Y.G. / Chen, E.S.W. / Huang, K.F. / Chen, C.J. / Tsai, M.D.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica Taiwan
National Health Research Institutes Taiwan
CitationJournal: Biochemistry / Year: 2015
Title: Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses.
Authors: Weng, J.H. / Hsieh, Y.C. / Huang, C.C. / Wei, T.Y. / Lim, L.H. / Chen, Y.H. / Ho, M.R. / Wang, I. / Huang, K.F. / Chen, C.J. / Tsai, M.D.
History
DepositionApr 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references

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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


Theoretical massNumber of molelcules
Total (without water)16,7201
Polymers16,7201
Non-polymers00
Water1448
1
A: TRAF-interacting protein with FHA domain-containing protein A

A: TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)33,4412
Polymers33,4412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1820 Å2
ΔGint-2 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.009, 39.009, 178.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TRAF-interacting protein with FHA domain-containing protein A / Putative MAPK-activating protein PM14 / Putative NF-kappa-B-activating protein 20 / TRAF2-binding protein


Mass: 16720.404 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIFA, T2BP / Plasmid: pET43.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CG3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 80mM LiCl, 0.2M trimethylamine N-oxide, 15% PEG 3350, 100mM HEPES
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9791, 0.9640
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.9641
ReflectionResolution: 2.7→20 Å / Num. obs: 4730 / % possible obs: 98.3 % / Redundancy: 8.8 % / Biso Wilson estimate: 37.77 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.023 / Rrim(I) all: 0.068 / Χ2: 0.859 / Net I/av σ(I): 29.857 / Net I/σ(I): 9.8 / Num. measured all: 41786
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.86.40.5484570.9180.2240.5960.76596.6
2.8-2.917.90.4164390.970.1540.4450.74498.7
2.91-3.048.90.3844630.9850.1340.4070.77798.1
3.04-3.29.60.264650.9910.0870.2740.86498.7
3.2-3.49.70.1794470.9940.060.1890.93698.7
3.4-3.669.70.1154740.9960.0390.1221.0198.8
3.66-4.039.60.0714650.9980.0250.0750.93799.1
4.03-4.69.50.0484780.9980.0160.0510.89898.8
4.6-5.7790.045030.9980.0140.0420.91898.4
5.77-2080.0255390.9990.0090.0260.65496.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.701→19.829 Å / FOM work R set: 0.7958 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 694 9.92 %
Rwork0.2263 6299 -
obs0.23 3602 84.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.63 Å2 / Biso mean: 40.62 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: final / Resolution: 2.701→19.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 0 8 1163
Biso mean---33.09 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121178
X-RAY DIFFRACTIONf_angle_d1.1651579
X-RAY DIFFRACTIONf_chiral_restr0.057170
X-RAY DIFFRACTIONf_plane_restr0.006203
X-RAY DIFFRACTIONf_dihedral_angle_d19.051450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7013-2.90930.2999740.302664071443
2.9093-3.2010.34161440.29691197134180
3.201-3.66160.30441460.24191477162399
3.6616-4.60370.23221680.199914771645100
4.6037-19.82930.22861620.20191508167099
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)
14.46081.2583-0.9893.2446-0.74383.502-0.51580.3751-0.5238-0.2580.4903-0.8940.10460.5019-0.04660.4446-0.1418-0.11280.555-0.12010.474.873813.777274.8133
22.1547-0.48630.01370.3233-0.75034.29910.1442-0.0807-0.3040.2280.184-0.2591.36220.1578-0.2140.3693-0.0906-0.10190.3185-0.08640.4212-0.1631.189675.4647
31.98190.98550.46327.7493-6.4148.8723-0.280.0741-1.19650.1923-0.2780.26760.9856-0.64330.06920.6751-0.3264-0.14170.53560.10280.2769-9.8093-3.047775.1776
42.01152.8738-1.94455.4921-4.16193.26580.18110.57860.6474-1.15260.1692-0.5381-0.418-0.07760.06550.1005-0.2522-0.46910.3827-0.0922-0.0934-2.946812.249764.2933
52.3335-0.0194-0.6893.0482-0.92583.0003-0.33210.34421.6193-0.6421-0.0060.5753-1.2027-1.02750.39140.3959-0.1135-0.28770.2868-0.06580.4738-3.108718.094463.1369
63.768-1.0314-1.17534.3163.34595.6505-0.0248-0.26280.435-0.91970.09420.37460.1822-0.72510.2570.1709-0.0037-0.09850.6979-0.04490.3093-15.85879.08471.8104
72.28662.41411.24072.53750.80421.25010.12890.77210.7620.660.20990.4752-2.0134-0.77960.0441-0.117-0.0519-0.08430.7329-0.01750.3174-10.727713.94167.1155
84.77292.1125-1.57948.9271-4.1426.28450.0665-1.2310.36041.45820.21470.7908-0.6885-0.6134-0.0980.35030.0141-0.01750.611-0.03860.3273-10.159911.786679.6417
93.07063.651-3.50194.084-3.81574.5449-0.2525-0.70720.35210.09820.1103-0.4778-0.2808-0.0486-0.00050.4964-0.1485-0.04150.6045-0.08970.3549-3.42812.914978.2454
101.1583-0.0054-0.49881.56130.53734.6582-0.2149-0.23860.49260.85550.82120.1178-0.37061.042-0.1687-0.0142-0.3284-0.27530.3536-0.12610.31413.31212.567176.0715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 10 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 103 )
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 113 )
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 121 )
9X-RAY DIFFRACTION9chain 'A' and (resid 122 through 129 )
10X-RAY DIFFRACTION10chain 'A' and (resid 130 through 149 )

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