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- PDB-6t5h: Human 14-3-3 sigma fused to the StARD1 peptide including phosphos... -

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Basic information

Entry
Database: PDB / ID: 6t5h
TitleHuman 14-3-3 sigma fused to the StARD1 peptide including phosphoserine-57
Components14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


positive regulation of bile acid biosynthetic process / cellular lipid metabolic process / regulation of steroid biosynthetic process / intracellular cholesterol transport / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / regulation of epidermal cell division ...positive regulation of bile acid biosynthetic process / cellular lipid metabolic process / regulation of steroid biosynthetic process / intracellular cholesterol transport / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / Mitochondrial protein degradation / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / cholesterol metabolic process / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrial intermembrane space / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / mitochondrial matrix / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Steroidogenic acute regulatory protein / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Steroidogenic acute regulatory protein / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily / 14-3-3 protein sigma / 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
IMIDAZOLE / TRIETHYLENE GLYCOL / 14-3-3 protein sigma / Steroidogenic acute regulatory protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSluchanko, N.N. / Tugaeva, K.V. / Titterington, J. / Antson, A.A.
Funding support Russian Federation, United Kingdom, 3items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10031 Russian Federation
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Febs J. / Year: 2020
Title: Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14-3-3 protein family.
Authors: Tugaeva, K.V. / Titterington, J. / Sotnikov, D.V. / Maksimov, E.G. / Antson, A.A. / Sluchanko, N.N.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
B: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0306
Polymers55,5102
Non-polymers5204
Water6,215345
1
A: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
hetero molecules

B: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0306
Polymers55,5102
Non-polymers5204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area3110 Å2
ΔGint6 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.170, 78.350, 76.060
Angle α, β, γ (deg.)90.000, 100.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial / Epithelial cell marker protein 1 / Stratifin / StAR / START domain-containing protein 1 / StARD1


Mass: 27755.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1, STAR, STARD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947, UniProt: P49675
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 279 K / Method: vapor diffusion / pH: 6.5
Details: 0.09 M NPS mix (0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate), 0.1 M Buffer mix (1.0 M Imidazole; MES), 25% v/v MPD; 25% polyethylene glycol 1000; 25% w/v ...Details: 0.09 M NPS mix (0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate), 0.1 M Buffer mix (1.0 M Imidazole; MES), 25% v/v MPD; 25% polyethylene glycol 1000; 25% w/v polyethylene glycol 3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.04→49.14 Å / Num. obs: 33161 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 36.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.122 / Net I/σ(I): 8.4
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3283 / CC1/2: 0.55 / Rrim(I) all: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
xia2data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OM0

5om0


Resolution: 2.04→49.13 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1632 4.92 %RANDOM
Rwork0.185 ---
obs0.187 33161 99.8 %-
Displacement parametersBiso max: 134.86 Å2 / Biso mean: 45.26 Å2 / Biso min: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1-11.8556 Å20 Å2-3.0318 Å2
2--1.7069 Å20 Å2
3----13.5624 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.04→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 82 345 4176
Biso mean--69.16 51.41 -
Num. residues----475
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1421SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes662HARMONIC5
X-RAY DIFFRACTIONt_it3888HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion490SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4855SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3888HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5262HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion18.25
LS refinement shellResolution: 2.04→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3055 29 4.37 %
Rwork0.2446 635 -
all0.247 664 -
obs--99.84 %

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