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- PDB-6sad: Structure of 14-3-3 gamma in complex with double phosphorylated c... -

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Basic information

Entry
Database: PDB / ID: 6sad
TitleStructure of 14-3-3 gamma in complex with double phosphorylated caspase-2 peptide on Ser139 and Ser164
Components
  • 14-3-3 protein gamma
  • Caspase-2
KeywordsSIGNALING PROTEIN / 14-3-3 protein / caspase-2 / complex
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / regulation of neuron differentiation / protein kinase C inhibitor activity ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / regulation of neuron differentiation / protein kinase C inhibitor activity / TP53 Regulates Transcription of Caspase Activators and Caspases / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / regulation of signal transduction / ectopic germ cell programmed cell death / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of apoptotic signaling pathway / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / extrinsic apoptotic signaling pathway in absence of ligand / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / insulin-like growth factor receptor binding / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein sequestering activity / protein kinase C binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / apoptotic signaling pathway / TP53 Regulates Metabolic Genes / regulation of synaptic plasticity / negative regulation of protein kinase activity / NOD1/2 Signaling Pathway / receptor tyrosine kinase binding / protein processing / cellular response to mechanical stimulus / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of PLK1 Activity at G2/M Transition / presynapse / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / focal adhesion / apoptotic process / DNA damage response / nucleolus / negative regulation of apoptotic process / enzyme binding / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-2 / Caspase recruitment domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase-2 / Caspase recruitment domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / 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 / Death-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Caspase-2 / 14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.753 Å
AuthorsKalabova, D. / Obsil, T. / Obsilova, V.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation17-00726S Czech Republic
CitationJournal: Febs J. / Year: 2020
Title: 14-3-3 protein binding blocks the dimerization interface of caspase-2.
Authors: Kalabova, D. / Filandr, F. / Alblova, M. / Petrvalska, O. / Horvath, M. / Man, P. / Obsil, T. / Obsilova, V.
History
DepositionJul 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 26, 2020Group: 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
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: Caspase-2


Theoretical massNumber of molelcules
Total (without water)58,1013
Polymers58,1013
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.425, 227.425, 73.335
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

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


Mass: 27004.426 Da / Num. of mol.: 2 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61981
#2: Protein/peptide Caspase-2 / / CASP-2 / Neural precursor cell expressed developmentally down-regulated protein 2 / NEDD-2 / Protease ICH-1


Mass: 4092.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Caspase-2 / Source: (synth.) Homo sapiens (human) / References: UniProt: P42575, caspase-2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.88 Å3/Da / Density % sol: 74.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, magnesium chloride, HEPES, 1,1,1,3,3,3-hexafluoropropan-2-ol

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.75→49.24 Å / Num. obs: 29434 / % possible obs: 99.88 % / Redundancy: 26.19 % / Biso Wilson estimate: 65.0466144142 Å2 / Rrim(I) all: 0.394 / Net I/σ(I): 10.17
Reflection shellResolution: 2.753→2.851 Å / Num. unique obs: 2885 / Rrim(I) all: 3.811

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 2.753→49.24 Å / SU ML: 0.464773020147 / Cross valid method: FREE R-VALUE / σ(F): 1.34964757315 / Phase error: 30.2319864885
RfactorNum. reflection% reflection
Rfree0.271048351218 1471 4.99830105335 %
Rwork0.229798205408 --
obs0.231868679263 29430 99.9185170096 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.8707773822 Å2
Refinement stepCycle: LAST / Resolution: 2.753→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 0 41 3808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001959664392623825
X-RAY DIFFRACTIONf_angle_d0.4435661344955193
X-RAY DIFFRACTIONf_chiral_restr0.0325417265851595
X-RAY DIFFRACTIONf_plane_restr0.00207001830772672
X-RAY DIFFRACTIONf_dihedral_angle_d23.20332786711391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.753-2.8420.3923455136141310.3512231623132494X-RAY DIFFRACTION99.7340425532
2.842-2.94350.384891020461320.3539422222472493X-RAY DIFFRACTION99.8858447489
2.9435-3.06140.3797832317491310.3181480121542497X-RAY DIFFRACTION100
3.0614-3.20070.3140991689821320.2978817939372503X-RAY DIFFRACTION100
3.2007-3.36940.3113288778021310.2786394859482504X-RAY DIFFRACTION99.9620637329
3.3694-3.58040.3173815750211320.2468039175482502X-RAY DIFFRACTION100
3.5804-3.85680.2885721998651340.2370774243092551X-RAY DIFFRACTION99.9627699181
3.8568-4.24470.2536012531581330.2041044511662512X-RAY DIFFRACTION99.9622071051
4.2447-4.85840.2201288165141340.1800051248122566X-RAY DIFFRACTION99.9629766753
4.8584-6.11930.2347776743281380.2225144215682598X-RAY DIFFRACTION99.8904709748
6.1193-49.240.2277674422371430.1881645083132739X-RAY DIFFRACTION99.7922437673

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