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- PDB-6t80: Human 14-3-3 sigma fused to the AANAT peptide including phosphose... -

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Basic information

Entry
Database: PDB / ID: 6t80
TitleHuman 14-3-3 sigma fused to the AANAT peptide including phosphoserine-205
Components
  • 14-3-3 protein sigma
  • AANAT peptide
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


indolalkylamine biosynthetic process / photoperiodism / aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / Serotonin and melatonin biosynthesis / arylamine N-acetyltransferase activity / response to prostaglandin E / N-terminal protein amino acid acetylation / response to copper ion ...indolalkylamine biosynthetic process / photoperiodism / aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / Serotonin and melatonin biosynthesis / arylamine N-acetyltransferase activity / response to prostaglandin E / N-terminal protein amino acid acetylation / response to copper ion / response to corticosterone / response to zinc ion / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / response to light stimulus / 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 / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to cAMP / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / 14-3-3 protein binding / stem cell proliferation / response to cytokine / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / response to insulin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to calcium ion / circadian rhythm / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / Acetyltransferase (GNAT) family / 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 ...14-3-3 protein sigma / Acetyltransferase (GNAT) family / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
14-3-3 protein sigma / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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: To Be Published
Title: Human 14-3-3 sigma fused to the AANAT peptide including phosphoserine-205
Authors: Sluchanko, N.N. / Tugaeva, K.V. / Titterington, J. / Antson, A.A.
History
DepositionOct 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 sigma
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: AANAT peptide
F: AANAT peptide
G: AANAT peptide
H: AANAT peptide


Theoretical massNumber of molelcules
Total (without water)111,5658
Polymers111,5658
Non-polymers00
Water362
1
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
G: AANAT peptide
H: AANAT peptide


Theoretical massNumber of molelcules
Total (without water)55,7824
Polymers55,7824
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: AANAT peptide
F: AANAT peptide


Theoretical massNumber of molelcules
Total (without water)55,7824
Polymers55,7824
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.260, 74.100, 102.090
Angle α, β, γ (deg.)90.000, 96.030, 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: This is a fusion protein with AANAT peptide, however it is not clear which chain this is linked to.
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
AANAT peptide


Mass: 1232.226 Da / Num. of mol.: 4
Fragment: Fused to 14-3-3 protein, but exact chain combinations is not known.
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: Q16613*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M MIB mix (sodium malonate dibasic monohydrate, imidazole, boric acid), 25% w/v polyethylene glycol 1500, pH 7.0

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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: 2.99→74.74 Å / Num. obs: 22776 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 74.11 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.124 / Rrim(I) all: 0.251 / Net I/σ(I): 3.8 / Num. measured all: 91716 / Scaling rejects: 52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.99-3.073.91.105648016800.4940.6511.288199.9
13.37-74.744.10.0811462820.9980.0430.0929.999.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LU2

5lu2


Resolution: 2.99→63.51 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.85 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.408
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1080 4.75 %RANDOM
Rwork0.2 ---
obs0.202 22756 99.6 %-
Displacement parametersBiso max: 210.09 Å2 / Biso mean: 89.9 Å2 / Biso min: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.3587 Å20 Å228.197 Å2
2--27.7185 Å20 Å2
3----20.3598 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.99→63.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 0 2 7240
Biso mean---50.11 -
Num. residues----933
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2617SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1266HARMONIC5
X-RAY DIFFRACTIONt_it7333HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion954SEMIHARMONIC5
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_contact9173SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7333HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9884HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion20.19
LS refinement shellResolution: 2.99→3.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3416 24 5.26 %
Rwork0.2336 432 -
all0.2405 456 -
obs--86.96 %
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)
11.25880.784-0.08493.3693-0.52761.7509-0.07530.0482-0.2029-0.0021-0.003-0.0786-0.0041-0.06730.0783-0.30450.0634-0.0153-0.1318-0.09320.032613.516-18.420439.6657
22.4504-1.09110.83714.13150.35551.66690.1104-0.02210.0221-0.1171-0.15870.04310.1118-0.09090.0484-0.3167-0.10480.0475-0.09320.0135-0.057810.778319.264836.9935
32.935-1.1637-0.2715.9807-0.4982.37010.19310.50270.43080.1059-0.3173-0.1608-0.1552-0.10120.1242-0.00790.0254-0.07950.25190.0940.034855.886138.2615.1872
43.8031-0.6723-1.23555.45881.5242.92150.13450.3152-0.5650.4841-0.43780.59840.2782-0.37040.30330.2223-0.14910.06220.1946-0.03520.31845.15481.767719.0446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 233
2X-RAY DIFFRACTION2{ B|* }B2 - 233
3X-RAY DIFFRACTION3{ C|* }C1 - 233
4X-RAY DIFFRACTION4{ D|* }D0 - 233

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