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- PDB-5oma: CH3 chimera of human 14-3-3 sigma with the StARD1 peptide includi... -

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Basic information

Entry
Database: PDB / ID: 5oma
TitleCH3 chimera of human 14-3-3 sigma with the StARD1 peptide including Ser57
Components
  • 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
  • Undetermined peptide
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


positive regulation of bile acid biosynthetic 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 bile acid biosynthetic 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 cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / cholesterol metabolic process / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / Mitochondrial protein degradation / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial intermembrane space / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / mitochondrial matrix / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / 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 domain / Delta-Endotoxin; domain 1 / START-like domain superfamily / 14-3-3 protein sigma ...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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / 14-3-3 protein sigma / Steroidogenic acute regulatory protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsSluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A.
Funding support Russian Federation, United Kingdom, 3items
OrganizationGrant numberCountry
Russian Science Foundation17-74-10053 Russian Federation
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners.
Authors: Sluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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 1.3Oct 9, 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 sigma,Steroidogenic acute regulatory protein, mitochondrial
B: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
C: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
D: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
H: Undetermined peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0128
Polymers111,6995
Non-polymers3133
Water181
1
A: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
C: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
H: Undetermined peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1244
Polymers56,0293
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
D: 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8894
Polymers55,6702
Non-polymers2182
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-13 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.251, 123.251, 162.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDH

#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: 27835.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: residues 75-77 were replaced by alanines to reduce surface entropy and improve crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1, STAR, STARD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947, UniProt: P49675
#2: Protein/peptide Undetermined peptide


Mass: 358.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Used to model a piece of the disordered peptide fused to the 14-3-3 protein core, of undetermined sequence. Most likely correspond to a continuation of chain D'.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 4 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-Trispropane pH 6.5, 0.2 M ammonium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 3.89→47 Å / Num. obs: 12047 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.71 % / Biso Wilson estimate: 136.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.265 / Rrim(I) all: 0.277 / Χ2: 0.902 / Net I/σ(I): 6.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.89-4.1312.6582.8850.9718700.2143.00699.2
4.13-4.4113.0752.0831.4817940.4332.16899.9
4.41-4.7612.5271.2272.4416630.7621.28100
4.76-5.2113.4050.9413.2315330.8310.979100
5.21-5.8112.9650.8343.4714250.8690.86999.9
5.81-6.712.6570.4825.7312470.9580.50399.9
6.7-8.1712.8570.20911.9910860.9920.21899.9
8.17-11.3911.8690.06428.618760.9990.067100
11.39-4710.8370.05734.845530.9980.0697

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LU1 (monomer)

5lu1


Resolution: 3.9→47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.751
RfactorNum. reflection% reflectionSelection details
Rfree0.248 951 7.96 %RANDOM
Rwork0.209 ---
obs0.212 11940 100 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 198.79 Å2 / Biso min: 86.62 Å2
Baniso -1Baniso -2Baniso -3
1-15.9644 Å20 Å20 Å2
2--15.9644 Å20 Å2
3----31.9289 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: final / Resolution: 3.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7268 0 18 1 7287
Biso mean--194.97 119.76 -
Num. residues----924
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2693SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes219HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1050HARMONIC5
X-RAY DIFFRACTIONt_it7383HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion952SEMIHARMONIC5
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_contact8242SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7383HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9939HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion22.13
LS refinement shellResolution: 3.9→4.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3041 236 8.46 %
Rwork0.2639 2552 -
all0.2672 2788 -
obs--100 %
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)
19.3315-1.5594-3.75934.87911.25335.0586-0.2284-0.3149-0.6308-0.32410.01280.20080.43290.59860.2156-0.19950.2030.1140.01320.231-0.1407-26.0815-11.7876-21.6359
211.18515.8208-1.595915.28750.11592.1468-0.0123-0.65570.27330.35760.2767-0.5646-0.6620.3725-0.26440.38270.11520.304-0.1104-0.03750.4593-25.387328.4016-21.6784
33.46740.43140.43364.0461-1.81763.46370.23810.18140.15870.4511-0.08440.5519-0.4584-0.4811-0.15380.08760.07930.0118-0.2798-0.04270.1739-52.2355-8.28025.5157
43.5063-0.7438-0.04336.8191-1.70753.21570.2996-0.4516-0.65030.4617-0.06140.56450.3002-0.3084-0.2382-0.0961-0.1686-0.2898-0.2080.25190.2918-53.1374-45.379623.7714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|235 }A1 - 235
2X-RAY DIFFRACTION2{ C|2 - C|231 }C2 - 231
3X-RAY DIFFRACTION3{ B|0 - B|236 }B0 - 236
4X-RAY DIFFRACTION4{ D|2 - D|231 }D2 - 231

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