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- PDB-1a38: 14-3-3 PROTEIN ZETA BOUND TO R18 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1a38
Title14-3-3 PROTEIN ZETA BOUND TO R18 PEPTIDE
Components
  • 14-3-3 PROTEIN ZETA
  • R18 PEPTIDE (PHCVPRDLSWLDLEANMCLP)
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / SIGNAL TRANSDUCTION / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
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 / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsPetosa, C. / Masters, S.C. / Pohl, J. / Wang, B. / Fu, H. / Liddington, R.C.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: 14-3-3zeta binds a phosphorylated Raf peptide and an unphosphorylated peptide via its conserved amphipathic groove.
Authors: Petosa, C. / Masters, S.C. / Bankston, L.A. / Pohl, J. / Wang, B. / Fu, H. / Liddington, R.C.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: 14-3-3Zeta Binds a Phosphorylated Raf Peptide and an Unphosphorylated Peptide Via its Conserved Amphipathic Groove
Authors: Petosa, C. / Masters, S.C. / Bankston, L.A. / Pohl, J. / Wang, B. / Fu, H. / Liddington, R.C.
History
DepositionJan 28, 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
P: R18 PEPTIDE (PHCVPRDLSWLDLEANMCLP)
B: 14-3-3 PROTEIN ZETA
Q: R18 PEPTIDE (PHCVPRDLSWLDLEANMCLP)


Theoretical massNumber of molelcules
Total (without water)60,2784
Polymers60,2784
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.520, 95.520, 235.360
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(-0.999912, -0.012104, 0.005414), (-0.012011, 0.999785, 0.016879), (-0.005617, 0.016813, -0.999843)62.486, 0.6475, -0.9617
2given(-0.997272, -0.002489, -0.073776), (0.004327, -0.999684, -0.024764), (-0.073691, -0.025016, 0.996967)61.6037, 79.7218, 3.4352
3given(0.998345, -0.005457, 0.057246), (-0.00623, -0.999892, 0.013332), (0.057167, -0.013667, -0.998271)0.5321, 80.1359, -1.5749

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Components

#1: Protein 14-3-3 PROTEIN ZETA


Mass: 27777.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P63103
#2: Protein/peptide R18 PEPTIDE (PHCVPRDLSWLDLEANMCLP)


Mass: 2361.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

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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: 5.14 Å3/Da / Density % sol: 76.08 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Liu, D., (1995) Nature, 376, 191.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
220-24 %PEG35001reservoir
3100 mMTris-HCl1reservoir
410 mM1reservoirMgCl2
51 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.35→20 Å / Num. obs: 17105 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 18.5
Reflection shellResolution: 3.35→3.5 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.32 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.39 1700 10 %BY RESOLUTION SHELLS
Rwork0.33 ---
obs0.33 17105 96.8 %-
Refinement stepCycle: LAST / Resolution: 3.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 0 0 3558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.71
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.72
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
Refine LS restraints NCSNCS model details: STRICT
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.3 / Rfactor Rfree: 0.35
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.71
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.72
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg2.7

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