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- PDB-9fvl: Dimeric 14-3-3 zeta in complex with unphosphorylated MAP2c peptide -

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Basic information

Entry
Database: PDB / ID: 9fvl
TitleDimeric 14-3-3 zeta in complex with unphosphorylated MAP2c peptide
Components
  • 14-3-3 protein zeta/delta
  • Isoform 3 of Microtubule-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Regulation / Mictorubule dynamics / Cytoskeleton / Phosphorylation
Function / homology
Function and homology information


CA3 pyramidal cell dendrite / primary dendrite / apical distal dendrite / positive regulation of anterograde synaptic vesicle transport / proximal neuron projection / : / positive regulation of anterograde dense core granule transport / regulation of organelle transport along microtubule / distal dendrite / basal dendrite ...CA3 pyramidal cell dendrite / primary dendrite / apical distal dendrite / positive regulation of anterograde synaptic vesicle transport / proximal neuron projection / : / positive regulation of anterograde dense core granule transport / regulation of organelle transport along microtubule / distal dendrite / basal dendrite / synaptic target recognition / Golgi reassembly / dendritic filopodium / negative regulation of axon extension / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / dystroglycan binding / proximal dendrite / respiratory system process / negative regulation of microtubule depolymerization / axon hillock / dendritic branch / regulation of synapse maturation / axon initial segment / tube formation / apical dendrite / microtubule bundle formation / Rap1 signalling / negative regulation of protein localization to nucleus / dendrite morphogenesis / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / negative regulation of microtubule polymerization / establishment of cell polarity / central nervous system neuron development / dendrite development / dendritic growth cone / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein targeting / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / dendrite cytoplasm / protein sequestering activity / ERK1 and ERK2 cascade / axonogenesis / nuclear periphery / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / dendritic shaft / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / microtubule cytoskeleton organization / ruffle membrane / neuron projection development / microtubule cytoskeleton / actin cytoskeleton / protein localization / melanosome / response to estradiol / regulation of protein localization / actin binding / cell body / microtubule binding / angiogenesis / DNA-binding transcription factor binding / blood microparticle / vesicle / microtubule / transmembrane transporter binding / calmodulin binding / postsynapse / postsynaptic density / neuron projection / cadherin binding / protein phosphorylation / protein domain specific binding / focal adhesion / neuronal cell body / dendrite / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / extracellular space
Similarity search - Function
MAP2/Tau projection / MAP2/Tau projection domain / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...MAP2/Tau projection / MAP2/Tau projection domain / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 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
Similarity search - Domain/homology
: / Microtubule-associated protein 2 / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsNarasimhan, S. / Jansen, S. / Zidek, L.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGA20-12669S Czech Republic
CitationJournal: Febs J. / Year: 2025
Title: Characterization of multiple binding sites on microtubule associated protein 2c recognized by dimeric and monomeric 14-3-3 zeta.
Authors: Jansen, S. / Narasimhan, S. / Cabre Fernandez, P. / Ilkovicova, L. / Kozelekova, A. / Kralova, K. / Hritz, J. / Zidek, L.
History
DepositionJun 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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/delta
B: 14-3-3 protein zeta/delta
E: Isoform 3 of Microtubule-associated protein 2
F: Isoform 3 of Microtubule-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1369
Polymers62,5744
Non-polymers5625
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Confirmed by Native gel studies and AUC studies
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-33 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.310, 69.108, 82.619
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28078.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: three residues are present at the N-terminal after TEV cleavage from the vector. 1Ser-2Val-3Asp
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P63104
#2: Protein/peptide Isoform 3 of Microtubule-associated protein 2 / MAP-2


Mass: 3208.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P15146
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH(7.5), 400 mM Sodium acetate, 8mM Cadmium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Nov 9, 2020 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.08→48.78 Å / Num. obs: 46317 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.111 / Χ2: 1.01 / Net I/σ(I): 11.7 / Num. measured all: 325384
Reflection shellResolution: 2.08→2.14 Å / % possible obs: 98.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.977 / Num. measured all: 24898 / Num. unique obs: 3557 / CC1/2: 0.805 / Rpim(I) all: 0.395 / Rrim(I) all: 1.055 / Χ2: 0.96 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
MOLREPphasing
XDSXDSGUIdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→48.78 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.88 / SU B: 5.074 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28255 2446 5.3 %RANDOM
Rwork0.23364 ---
obs0.23618 43853 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.105 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.08→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 5 245 3989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123787
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163663
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.8595086
X-RAY DIFFRACTIONr_angle_other_deg0.621.7928452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.41524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10710743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02841
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4073.5711859
X-RAY DIFFRACTIONr_mcbond_other3.4063.5711859
X-RAY DIFFRACTIONr_mcangle_it4.6566.382315
X-RAY DIFFRACTIONr_mcangle_other4.6556.3832316
X-RAY DIFFRACTIONr_scbond_it5.0534.141928
X-RAY DIFFRACTIONr_scbond_other5.0524.1421929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4377.3932772
X-RAY DIFFRACTIONr_long_range_B_refined9.77738.614536
X-RAY DIFFRACTIONr_long_range_B_other9.77638.624537
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.082→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 178 -
Rwork0.284 3235 -
obs--98.98 %

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