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- PDB-1a37: 14-3-3 PROTEIN ZETA BOUND TO PS-RAF259 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1a37
Title14-3-3 PROTEIN ZETA BOUND TO PS-RAF259 PEPTIDE
Components
  • 14-3-3 PROTEIN ZETA
  • PS-RAF259 PEPTIDE LSQRQRST(SEP)TPNVHM
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / SIGNAL TRANSDUCTION / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
Function / homology14-3-3 protein, conserved site / 14-3-3 domain / TP53 Regulates Metabolic Genes / RHO GTPases activate PKNs / Interleukin-3, Interleukin-5 and GM-CSF signaling / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Rap1 signalling / Deactivation of the beta-catenin transactivating complex / Translocation of SLC2A4 (GLUT4) to the plasma membrane ...14-3-3 protein, conserved site / 14-3-3 domain / TP53 Regulates Metabolic Genes / RHO GTPases activate PKNs / Interleukin-3, Interleukin-5 and GM-CSF signaling / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Rap1 signalling / Deactivation of the beta-catenin transactivating complex / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Activation of BAD and translocation to mitochondria / 14-3-3 proteins signature 2. / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 domain superfamily / 14-3-3 protein / NOTCH4 Activation and Transmission of Signal to the Nucleus / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of synapse maturation / hippocampal mossy fiber to CA3 synapse / synaptic target recognition / regulation of cell death / Golgi reassembly / glutamatergic synapse / establishment of Golgi localization / protein targeting / melanosome / ion channel binding / transcription factor binding / ubiquitin protein ligase binding / protein domain specific binding / protein kinase binding / identical protein binding / nucleus / 14-3-3 protein zeta/delta
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 3.6 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 1998 / Release: Mar 2, 1999
RevisionDateData content typeGroupProviderType
1.0Mar 2, 1999Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 16, 2011Structure modelOther
1.4Aug 17, 2016Structure modelStructure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA
P: PS-RAF259 PEPTIDE LSQRQRST(SEP)TPNVHM
B: 14-3-3 PROTEIN ZETA
Q: PS-RAF259 PEPTIDE LSQRQRST(SEP)TPNVHM


Theoretical massNumber of molelcules
Total (without water)59,2364
Polyers59,2364
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)94.730, 94.730, 250.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP 65

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Components

#1: Protein/peptide 14-3-3 PROTEIN ZETA


Mass: 27777.092 Da / Num. of mol.: 2
Details: COMPLEXED WITH PHOSPHOSERINE-CONTAINING PEPTIDE DERIVED FROM RAF
Source: (gene. exp.) Bos taurus (cattle) / Genus: Bos / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P63103
#2: Protein/peptide PS-RAF259 PEPTIDE LSQRQRST(SEP)TPNVHM


Mass: 1840.951 Da / Num. of mol.: 2

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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: 5.49 / Density percent sol: 77.58 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Liu, D., (1995) Nature, 376, 191.
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Jun 1, 1997
RadiationMonochromator: NI FILTER / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 3.6 Å / D resolution low: 20 Å / Number obs: 14700 / Observed criterion sigma I: 0 / Rsym value: 0.072 / NetI over sigmaI: 20 / Redundancy: 4.3 % / Percent possible obs: 99
Reflection shellHighest resolution: 3.6 Å / Lowest resolution: 3.8 Å / MeanI over sigI obs: 7 / Rsym value: 0.258 / Redundancy: 3.7 % / Percent possible all: 98.8
Reflection
*PLUS
D resolution high: 3.6 Å / D resolution low: 2 Å / Number obs: 14696 / Percent possible obs: 99.5 / Rmerge I obs: 0.07

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: BY RESOLUTION SHELLS / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.36 / R factor R work: 0.32 / R factor obs: 0.32 / Highest resolution: 3.6 Å / Lowest resolution: 20 Å / Number reflection obs: 14700 / Percent reflection R free: 10 / Percent reflection obs: 98.9
Refine hist #LASTHighest resolution: 3.6 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 3194 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3194
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor obs: 0.31 / Lowest resolution: 2 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.9

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