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- PDB-1a4o: 14-3-3 PROTEIN ZETA ISOFORM -

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Basic information

Entry
Database: PDB / ID: 1a4o
Title14-3-3 PROTEIN ZETA ISOFORM
Components14-3-3 PROTEIN ZETA
KeywordsSIGNAL TRANSDUCTION
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / GP1b-IX-V activation signalling / Deactivation of the beta-catenin transactivating complex / regulation of programmed cell death / synaptic target recognition ...KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / GP1b-IX-V activation signalling / Deactivation of the beta-catenin transactivating complex / regulation of programmed cell death / synaptic target recognition / Rap1 signalling / TP53 Regulates Metabolic Genes / Golgi reassembly / Interleukin-3, Interleukin-5 and GM-CSF signaling / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / negative regulation of protein localization to nucleus / phosphoserine residue binding / regulation of ERK1 and ERK2 cascade / protein targeting / cellular response to glucose starvation / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / lung development / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / intracellular protein localization / melanosome / angiogenesis / protein phosphatase binding / DNA-binding transcription factor binding / transmembrane transporter binding / protein phosphorylation / protein domain specific binding / ubiquitin protein ligase binding / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 zeta/delta
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsLiu, D. / Bienkowska, J. / Petosa, C. / Collier, R.J. / Fu, H. / Liddington, R.C.
CitationJournal: Nature / Year: 1995
Title: Crystal structure of the zeta isoform of the 14-3-3 protein.
Authors: Liu, D. / Bienkowska, J. / Petosa, C. / Collier, R.J. / Fu, H. / Liddington, R.
History
DepositionFeb 1, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA
B: 14-3-3 PROTEIN ZETA
C: 14-3-3 PROTEIN ZETA
D: 14-3-3 PROTEIN ZETA


Theoretical massNumber of molelcules
Total (without water)111,1084
Polymers111,1084
Non-polymers00
Water00
1
A: 14-3-3 PROTEIN ZETA
B: 14-3-3 PROTEIN ZETA


Theoretical massNumber of molelcules
Total (without water)55,5542
Polymers55,5542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-6 kcal/mol
Surface area20660 Å2
MethodPISA
2
C: 14-3-3 PROTEIN ZETA
D: 14-3-3 PROTEIN ZETA


Theoretical massNumber of molelcules
Total (without water)55,5542
Polymers55,5542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-5 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.900, 94.900, 236.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99992, 0.00362, 0.01179), (0.00353, 0.99996, -0.0076), (-0.01182, -0.00756, -0.9999)33.077, 0.10009, 38.7624
2given(-0.99748, -0.0034, 0.07089), (0.00539, -0.9996, 0.02791), (0.07076, 0.02822, 0.99709)31.94674, 84.1939, -2.36641
3given(0.99715, 0.01041, -0.07473), (0.01081, -0.99993, 0.00496), (-0.07467, -0.00575, -0.99719)0.66512, 84.6761, 39.7839
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO DIMERS ARRANGED WITH APPROXIMATE 222 POINT SYMMETRY. MONOMERS A AND B FORM ONE DIMER; C AND D FORM THE OTHER.

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Components

#1: Protein
14-3-3 PROTEIN ZETA


Mass: 27777.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P63103

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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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-10 mg/mlprotein1drop
220-24 %PEG35001reservoir
3100 mMTris-HCl1reservoirpH8.5
410 mM1reservoirMgCl2
51 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.01
DetectorDate: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 28237 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Rsym value: 0.074 / Net I/σ(I): 11.6
Reflection
*PLUS
Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.345 -7.8 %BY RESOLUTION SHELLS
Rwork0.31 ---
obs0.31 28237 96.4 %-
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 0 0 6364
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.18
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.56
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.411 --
Rwork0.39 3040 -
obs--87.5 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.31 / Rfactor Rwork: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.39

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