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- PDB-4ym4: Truncated Human TIFA in complex with its Thr9 phosphorylated N-te... -

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Basic information

Entry
Database: PDB / ID: 4ym4
TitleTruncated Human TIFA in complex with its Thr9 phosphorylated N-terminal peptide 1-15
Components(TRAF-interacting protein with FHA domain-containing protein A) x 2
KeywordsSIGNALING PROTEIN / Complex / 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: 3.12 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
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 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
B: TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)18,3042
Polymers18,3042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-3 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.205, 113.205, 113.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232

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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: 16848.533 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-150
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: Protein/peptide TRAF-interacting protein with FHA domain-containing protein A / Thr9 phosphorylated N-terminal peptide


Mass: 1455.349 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CG3

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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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-malic acid pH7.0 / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 4922 / % possible obs: 100 % / Redundancy: 21.8 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.035 / Rrim(I) all: 0.164 / Χ2: 0.947 / Net I/av σ(I): 23.556 / Net I/σ(I): 6.3 / Num. measured all: 107113
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
3.1-3.2119.20.8854710.9040.2060.9090.955
3.21-3.3422.10.6714780.9390.1450.6870.954
3.34-3.4923.10.454740.9950.0950.4610.923
3.49-3.6723.10.3254780.9840.0690.3320.948
3.67-3.923.10.2144800.9940.0450.2190.985
3.9-4.222.80.1524790.9950.0320.1550.955
4.2-4.6222.50.0974880.9970.0210.0990.952
4.62-5.2722.20.0795000.9980.0170.0810.917
5.27-6.6121.30.0995130.9980.0220.1021.111
6.61-2018.80.045610.9990.0090.0410.769

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 3.12→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 226 4.7 %RANDOM
Rwork0.2134 ---
obs0.2145 4543 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 186.46 Å2 / Biso mean: 44.632 Å2 / Biso min: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.12→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 0 1240
Num. residues----153
LS refinement shellResolution: 3.121→3.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 17 -
Rwork0.316 324 -
all-341 -
obs--100 %

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