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- PDB-6gkf: 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: 6gkf
TitleStructure of 14-3-3 gamma in complex with caspase-2 14-3-3 binding motif Ser139
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 / positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / NADE modulates death signalling / luteolysis / neural retina development / positive regulation of T cell mediated immune response to tumor cell / execution phase of apoptosis / regulation of neuron differentiation ...caspase-2 / endopeptidase complex / positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / NADE modulates death signalling / luteolysis / neural retina development / positive regulation of T cell mediated immune response to tumor cell / execution phase of apoptosis / regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / protein kinase C inhibitor activity / extrinsic apoptotic signaling pathway in absence of ligand / Regulation of localization of FOXO transcription factors / regulation of signal transduction / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of protein kinase activity / insulin-like growth factor receptor binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / negative regulation of TORC1 signaling / apoptotic signaling pathway / AURKA Activation by TPX2 / protein kinase C binding / protein processing / DNA damage response, signal transduction by p53 class mediator / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to mechanical stimulus / regulation of synaptic plasticity / protein sequestering activity / receptor tyrosine kinase binding / NOD1/2 Signaling Pathway / intracellular protein localization / positive regulation of T cell activation / SPOP-mediated proteasomal degradation of PD-L1(CD274) / positive regulation of neuron apoptotic process / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / regulation of protein localization / presynapse / positive regulation of apoptotic process / apoptotic process / mitochondrial matrix / protein domain specific binding / focal adhesion / cysteine-type endopeptidase activity / DNA damage response / negative regulation of apoptotic process / nucleolus / enzyme binding / mitochondrion / RNA binding / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / 14-3-3 domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / 14-3-3 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 / Delta-Endotoxin; domain 1 / 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: 2.598 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: 14-3-3 protein gamma
E: 14-3-3 protein gamma
G: 14-3-3 protein gamma
B: 14-3-3 protein gamma
D: 14-3-3 protein gamma
F: 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
O: Caspase-2
P: Caspase-2


Theoretical massNumber of molelcules
Total (without water)224,28416
Polymers224,28416
Non-polymers00
Water2,054114
1
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
I: Caspase-2
J: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0714
Polymers56,0714
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
K: Caspase-2
L: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0714
Polymers56,0714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma
M: Caspase-2
N: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0714
Polymers56,0714
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 14-3-3 protein gamma
H: 14-3-3 protein gamma
O: Caspase-2
P: Caspase-2


Theoretical massNumber of molelcules
Total (without water)56,0714
Polymers56,0714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.540, 122.540, 312.013
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 / Plasmid: pET15-b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61981
#2: Protein/peptide
Caspase-2


Mass: 1031.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42575*PLUS, caspase-2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 4000, TRIS-HCl, sodium acetate

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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: 2.598→48.183 Å / Num. obs: 74062 / % possible obs: 99.83 % / Redundancy: 26.7 % / Biso Wilson estimate: 59.68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1293 / Rpim(I) all: 0.02535 / Rrim(I) all: 0.1318 / Net I/σ(I): 23.63
Reflection shellResolution: 2.598→2.691 Å / Redundancy: 27.5 % / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 7245 / CC1/2: 0.849 / Rpim(I) all: 0.3199 / Rrim(I) all: 1.689 / % possible all: 99.59

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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: 2.598→48.183 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 2098 2.84 %Random selection
Rwork0.2415 ---
obs0.2428 73994 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.598→48.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13994 0 0 114 14108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214190
X-RAY DIFFRACTIONf_angle_d0.36719261
X-RAY DIFFRACTIONf_dihedral_angle_d19.1265071
X-RAY DIFFRACTIONf_chiral_restr0.0312233
X-RAY DIFFRACTIONf_plane_restr0.0022490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5976-2.6580.35341350.31254644X-RAY DIFFRACTION98
2.658-2.72450.31431380.29324729X-RAY DIFFRACTION100
2.7245-2.79810.3051380.28844714X-RAY DIFFRACTION100
2.7981-2.88050.36961380.30514712X-RAY DIFFRACTION100
2.8805-2.97340.37861380.31714752X-RAY DIFFRACTION100
2.9734-3.07970.35471390.29464735X-RAY DIFFRACTION100
3.0797-3.2030.32151380.27844731X-RAY DIFFRACTION100
3.203-3.34870.32951390.27674757X-RAY DIFFRACTION100
3.3487-3.52520.31821390.26924771X-RAY DIFFRACTION100
3.5252-3.7460.29421390.24344773X-RAY DIFFRACTION100
3.746-4.03510.27531410.22944813X-RAY DIFFRACTION100
4.0351-4.44090.22641410.21584822X-RAY DIFFRACTION100
4.4409-5.08290.2881420.21974874X-RAY DIFFRACTION100
5.0829-6.40150.30931430.25014909X-RAY DIFFRACTION100
6.4015-48.19150.23931500.19085160X-RAY DIFFRACTION100

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