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- PDB-6t5f: Human 14-3-3 sigma fused to the StARD1 peptide including phosphos... -

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Basic information

Entry
Database: PDB / ID: 6t5f
TitleHuman 14-3-3 sigma fused to the StARD1 peptide including phosphoserine-195
Components
  • 14-3-3 protein sigma
  • StARD1 peptide
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


positive regulation of bile acid biosynthetic process / : / intracellular cholesterol transport / regulation of steroid biosynthetic process / 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 / : / intracellular cholesterol transport / regulation of steroid biosynthetic process / 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 cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / negative regulation of innate immune response / protein sequestering activity / Mitochondrial protein degradation / protein kinase A signaling / protein export from nucleus / cholesterol metabolic process / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / mitochondrial intermembrane space / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / 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 / cytosol / cytoplasm
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. / 14-3-3 protein sigma / START-like domain superfamily / 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. / 14-3-3 protein sigma / START-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
Similarity search - Domain/homology
14-3-3 protein sigma / Steroidogenic acute regulatory protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: StARD1 peptide
F: StARD1 peptide
G: StARD1 peptide
H: StARD1 peptide


Theoretical massNumber of molelcules
Total (without water)112,4188
Polymers112,4188
Non-polymers00
Water1,946108
1
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
G: StARD1 peptide
H: StARD1 peptide


Theoretical massNumber of molelcules
Total (without water)56,2094
Polymers56,2094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-17 kcal/mol
Surface area23790 Å2
MethodPISA
2
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: StARD1 peptide
F: StARD1 peptide


Theoretical massNumber of molelcules
Total (without water)56,2094
Polymers56,2094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-17 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 74.950, 104.380
Angle α, β, γ (deg.)90.000, 97.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26659.018 Da / Num. of mol.: 4
Fragment: Human 14-3-3 sigma protein is fused to the StARD1 peptide, though not clear which chains connect together in the structure.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide
StARD1 peptide


Mass: 1445.541 Da / Num. of mol.: 4
Fragment: Human 14-3-3 sigma protein is fused to the StARD1 peptide, though not clear which chains connect together in the structure.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P49675*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.63→53.51 Å / Num. obs: 35345 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 63.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.17 / Net I/σ(I): 5.4
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 4 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3496 / CC1/2: 0.48 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5om0


Resolution: 2.63→51.69 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 0.729 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.675 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.318
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1811 5.12 %RANDOM
Rwork0.217 ---
obs0.219 35345 99.7 %-
Displacement parametersBiso max: 176.3 Å2 / Biso mean: 80.24 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1--14.1372 Å20 Å215.9062 Å2
2--17.385 Å20 Å2
3----3.2478 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.63→51.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7555 0 0 111 7666
Biso mean---57.09 -
Num. residues----965
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2786SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1312HARMONIC5
X-RAY DIFFRACTIONt_it7658HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion989SEMIHARMONIC5
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_contact8741SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7658HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10306HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion19.55
LS refinement shellResolution: 2.63→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2707 40 5.66 %
Rwork0.2435 667 -
all0.2453 707 -
obs--88.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12670.60230.17263.9236-0.882.2008-0.0390.1051-0.03870.0999-0.0531-0.0964-0.0472-0.10010.092-0.19220.0599-0.2215-0.2886-0.10870.251611.9238-18.709440.4305
22.1463-0.99311.20883.67680.51261.56780.1956-0.0315-0.08030.1369-0.1512-0.06860.09070.0208-0.0444-0.1564-0.1103-0.1636-0.26620.05740.12869.852619.232337.9051
31.5681-0.1087-0.13052.2972-0.49921.24760.17010.41120.41050.0466-0.1303-0.0645-0.1728-0.1793-0.03990.06010.1095-0.18620.0330.05360.256656.024138.059115.3425
44.44830.80020.04273.31870.52731.9486-0.05350.2321-0.55410.44110.0590.12230.3862-0.2474-0.00550.0929-0.0589-0.1816-0.0341-0.01340.257245.56931.437118.6809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 233
2X-RAY DIFFRACTION2{ B|* }B0 - 234
3X-RAY DIFFRACTION3{ C|* }C-1 - 233
4X-RAY DIFFRACTION4{ D|* }D1 - 233

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