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- PDB-5iqp: 14-3-3 PROTEIN TAU ISOFORM -

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Basic information

Entry
Database: PDB / ID: 5iqp
Title14-3-3 PROTEIN TAU ISOFORM
Components14-3-3 protein theta
KeywordsSIGNALING PROTEIN / MULTIPLE SIGNALLING PATHWAYS / PHOSPHORYLATION / BINDING TO KINASE
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / small GTPase-mediated signal transduction / Regulation of localization of FOXO transcription factors / protein targeting / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / substantia nigra development ...negative regulation of monoatomic ion transmembrane transport / small GTPase-mediated signal transduction / Regulation of localization of FOXO transcription factors / protein targeting / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / substantia nigra development / 14-3-3 protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / transmembrane transporter binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / synapse / signal transduction / protein-containing complex / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
14-3-3 theta / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily ...14-3-3 theta / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein theta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.602 Å
AuthorsXiao, B. / Smerdon, S.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 1995
Title: Structure of a 14-3-3 protein and implications for coordination of multiple signalling pathways
Authors: Xiao, B. / Smerdon, S.J. / Jones, D.H. / Dodson, G.G. / Soneji, Y. / Aitken, A. / Gamblin, S.J.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein theta
B: 14-3-3 protein theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7834
Polymers55,5902
Non-polymers1922
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-39 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.290, 79.300, 101.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein theta / 14-3-3 protein T-cell / 14-3-3 protein tau / Protein HS1


Mass: 27795.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-CELL / Gene: YWHAQ / Production host: Escherichia coli (E. coli) / References: UniProt: P27348
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.3 Å3/Da / Density % sol: 46.9 % / Description: needle-like
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 24% PEG4K, 140 mM LI2SO4, 4 % of SATURATED NACL IN 80 mM MES AT pH 6.4; PROTEIN 7 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.602→14.967 Å / Num. obs: 17742 / % possible obs: 99.69 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.9
Reflection shellResolution: 2.602→2.69 Å / Rmerge(I) obs: 0.295

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.602→14.967 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2393 938 5.29 %
Rwork0.1863 --
obs0.1891 17742 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.602→14.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 10 169 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023682
X-RAY DIFFRACTIONf_angle_d0.3984963
X-RAY DIFFRACTIONf_dihedral_angle_d13.9942259
X-RAY DIFFRACTIONf_chiral_restr0.032561
X-RAY DIFFRACTIONf_plane_restr0.002637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6016-2.73790.29591440.22662337X-RAY DIFFRACTION99
2.7379-2.90830.30511400.21992345X-RAY DIFFRACTION100
2.9083-3.1310.26371300.21952367X-RAY DIFFRACTION100
3.131-3.44260.25771200.20362394X-RAY DIFFRACTION100
3.4426-3.93280.2111350.16972410X-RAY DIFFRACTION100
3.9328-4.92540.19791300.14972416X-RAY DIFFRACTION100
4.9254-14.96740.22781390.17922535X-RAY DIFFRACTION100
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)
12.82360.5979-0.4442.7725-1.44222.60280.07540.1765-0.0542-0.0875-0.06280.02730.16440.10470.00120.1884-0.00020.03320.2021-0.04240.148850.248138.14432.8504
24.00280.2009-0.65222.26670.97312.8194-0.22930.3589-0.1719-0.1546-0.01770.06090.3056-0.3630.13080.1548-0.03180.0230.1781-0.00310.220834.161237.171137.637
32.88550.44970.71212.39590.20553.19060.0118-0.16940.16980.0794-0.1515-0.1903-0.07390.14850.13530.1281-0.0130.00710.17380.01180.154235.871148.536249.9165
47.1176-1.3086-3.44564.21160.83.2020.10550.56590.3232-0.27980.16580.28870.0239-0.1212-0.12480.2174-0.01550.02560.2435-0.00810.17963.873949.733219.2458
53.07731.0346-0.27291.4692-1.18034.06410.0777-0.1233-0.60040.091-0.006-0.38770.04420.1353-0.01090.21240.0042-0.03710.1641-0.02830.348972.136139.24132.8302
64.60571.00020.2531.5241.13493.0626-0.18490.2573-0.5071-0.09210.2464-0.44480.10550.3395-0.07860.15610.02950.01880.23-0.0670.253985.815747.034428.3157
73.49640.2744-0.07542.34491.3472.1529-0.1034-0.19940.1091-0.21370.10490.0509-0.0559-0.1267-0.0540.14980.0242-0.02580.24150.0240.152887.033458.003238.5144
84.1424-0.93960.56767.0897-2.34683.9865-0.4536-0.11650.14270.84350.3490.2588-0.9789-0.60450.16320.26860.092-0.00490.2461-0.0590.227479.077861.631741.7399
90.7297-0.0468-0.17820.123-0.0790.07250.00390.0853-0.0695-0.085-0.0299-0.0820.0447-0.05460.02890.2376-0.03170.02710.2335-0.02790.190360.241845.066835.7804
100.1536-0.4839-0.13231.56220.3210.42450.0196-0.18510.2181-0.28160.2066-0.55280.2198-0.32490.28280.278-0.10350.08510.7475-0.03730.468559.852247.748238.4654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:103)
2X-RAY DIFFRACTION2(chain A and resid 104:159)
3X-RAY DIFFRACTION3(chain A and resid 160:230)
4X-RAY DIFFRACTION4(chain B and resid 1:32)
5X-RAY DIFFRACTION5(chain B and resid 33:103)
6X-RAY DIFFRACTION6(chain B and resid 104:159)
7X-RAY DIFFRACTION7(chain B and resid 160:207)
8X-RAY DIFFRACTION8(chain B and resid 208:230)
9X-RAY DIFFRACTION9(chain W and resid 301:469)
10X-RAY DIFFRACTION10(chain X and resid 601:602)

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