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- PDB-6gkg: Structure of 14-3-3 gamma in complex with caspase-2 14-3-3 bindin... -

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Basic information

Entry
Database: PDB / ID: 6gkg
TitleStructure of 14-3-3 gamma in complex with caspase-2 14-3-3 binding motif Ser164
Components
  • 14-3-3 protein gamma
  • Caspase-2
KeywordsSIGNALING PROTEIN / complex / phosphorylation / 14-3-3 protein / caspase-2
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: 2.847 Å
AuthorsAlblova, M. / Obsil, T. / Obsilova, V.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation17-00726S Czech Republic
CitationJournal: FEBS J. / Year: 2018
Title: 14-3-3 protein masks the nuclear localization sequence of caspase-2.
Authors: Smidova, A. / Alblova, M. / Kalabova, D. / Psenakova, K. / Rosulek, M. / Herman, P. / Obsil, T. / Obsilova, V.
History
DepositionMay 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Jan 17, 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: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma
G: 14-3-3 protein gamma
H: 14-3-3 protein gamma
I: Caspase-2
J: Caspase-2
K: Caspase-2
L: Caspase-2
M: Caspase-2
N: Caspase-2


Theoretical massNumber of molelcules
Total (without water)222,17314
Polymers222,17314
Non-polymers00
Water0
1
A: 14-3-3 protein gamma
E: 14-3-3 protein gamma
I: Caspase-2
J: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0554
Polymers56,0554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 14-3-3 protein gamma
F: 14-3-3 protein gamma
K: Caspase-2
L: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0554
Polymers56,0554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 14-3-3 protein gamma
G: 14-3-3 protein gamma
M: Caspase-2
N: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0554
Polymers56,0554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 14-3-3 protein gamma
H: 14-3-3 protein gamma


Theoretical massNumber of molelcules
Total (without water)54,0092
Polymers54,0092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.987, 121.987, 311.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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.: 8 / Mutation: S235Stop
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 /


Mass: 1022.992 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42575*PLUS, caspase-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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5 / Details: Tris-HCl, PEG 4000, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 7, 2018 / Details: Sagitally bended Si111 crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.847→47.989 Å / Num. obs: 55837 / % possible obs: 99.79 % / Redundancy: 26.5 % / Biso Wilson estimate: 60.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.3057 / Rpim(I) all: 0.06011 / Rrim(I) all: 0.3117 / Net I/σ(I): 12.86
Reflection shellResolution: 2.847→2.949 Å / Redundancy: 26.7 % / Rmerge(I) obs: 2.53 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 5427 / CC1/2: 0.564 / Rpim(I) all: 0.4947 / Rrim(I) all: 2.578 / % possible all: 99.18

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 2.847→47.989 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 2101 3.76 %
Rwork0.2312 --
obs0.2333 55829 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.847→47.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14100 0 0 0 14100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00114292
X-RAY DIFFRACTIONf_angle_d0.33219369
X-RAY DIFFRACTIONf_dihedral_angle_d19.1815180
X-RAY DIFFRACTIONf_chiral_restr0.032239
X-RAY DIFFRACTIONf_plane_restr0.0022496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8473-2.91360.39661370.33173498X-RAY DIFFRACTION99
2.9136-2.98640.37571370.32433502X-RAY DIFFRACTION100
2.9864-3.06710.35831380.29363532X-RAY DIFFRACTION100
3.0671-3.15740.33391370.28113499X-RAY DIFFRACTION100
3.1574-3.25930.34221380.27063529X-RAY DIFFRACTION99
3.2593-3.37570.32571390.26423556X-RAY DIFFRACTION100
3.3757-3.51080.29931380.24493542X-RAY DIFFRACTION100
3.5108-3.67060.28531390.23363562X-RAY DIFFRACTION100
3.6706-3.8640.28961380.22433529X-RAY DIFFRACTION100
3.864-4.1060.27061410.20853590X-RAY DIFFRACTION100
4.106-4.42280.24751400.1983585X-RAY DIFFRACTION100
4.4228-4.86750.25431410.20493621X-RAY DIFFRACTION100
4.8675-5.57090.32611430.22273643X-RAY DIFFRACTION100
5.5709-7.01530.28651420.24533651X-RAY DIFFRACTION99
7.0153-47.9960.23221530.19753889X-RAY DIFFRACTION100

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