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- PDB-4dau: Structure of 14-3-3 sigma in complex with PADI6 14-3-3 binding motif I -

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Basic information

Entry
Database: PDB / ID: 4dau
TitleStructure of 14-3-3 sigma in complex with PADI6 14-3-3 binding motif I
Components
  • 14-3-3 protein sigma
  • Peptidylarginine Deiminase type VI
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / 14-3-3 fold / protein-protein interaction / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of translation by machinery localization / cytoplasm organization / protein-arginine deiminase / cortical granule / protein-arginine deiminase activity / embryonic cleavage / intermediate filament cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation ...regulation of translation by machinery localization / cytoplasm organization / protein-arginine deiminase / cortical granule / protein-arginine deiminase activity / embryonic cleavage / intermediate filament cytoskeleton / 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 / Chromatin modifying enzymes / 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 / RHO GTPases activate PKNs / cytoskeleton organization / protein kinase A signaling / 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 / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / calcium ion 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
Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / 14-3-3 domain ...Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Cupredoxin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Protein-arginine deiminase type-6 / Protein-arginine deiminase type-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRose, R. / Rose, M. / Ottmann, C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI.
Authors: Rose, R. / Rose, M. / Ottmann, C.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Peptidylarginine Deiminase type VI


Theoretical massNumber of molelcules
Total (without water)27,9242
Polymers27,9242
Non-polymers00
Water6,990388
1
A: 14-3-3 protein sigma
B: Peptidylarginine Deiminase type VI

A: 14-3-3 protein sigma
B: Peptidylarginine Deiminase type VI


Theoretical massNumber of molelcules
Total (without water)55,8494
Polymers55,8494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4040 Å2
ΔGint-24 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.220, 110.240, 61.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-560-

HOH

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Components

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


Mass: 26414.787 Da / Num. of mol.: 1 / Fragment: UNP residues 1-231
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 Peptidylarginine Deiminase type VI


Mass: 1509.621 Da / Num. of mol.: 1 / Fragment: 14-3-3 binding motif I (UNP residues 1-13) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q330K5, UniProt: Q6TGC4*PLUS, protein-arginine deiminase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26.6% v/v PEG400, 0.19 M calcium chloride, 5% v/v glycerol, 0.095 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 19140 / Num. obs: 18642 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.414 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.30.2066.52198326233196.6
2.3-2.60.09811.55119013757198.2
2.6-30.11215.07104253003198.8
3-3.50.07221.2573092080198.8
3.5-40.05926.2541041172198.2
4-50.05626.8540451170197.4
5-100.05326.1237971089195.5
10-150.03833.38379112189.6
15-200.04929.868226186.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
PHASERphasing
RefinementStarting model: PDB ENTRY 3IQV

3iqv


Resolution: 2→19.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.783 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 932 5 %RANDOM
Rwork0.1665 ---
all0.1696 ---
obs0.1696 18641 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.71 Å2 / Biso mean: 17.9336 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 0 388 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221954
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.9792646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15824.61591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26215.04371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3071514
X-RAY DIFFRACTIONr_chiral_restr0.1430.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021474
X-RAY DIFFRACTIONr_mcbond_it1.1081.51217
X-RAY DIFFRACTIONr_mcangle_it1.97321960
X-RAY DIFFRACTIONr_scbond_it3.8173737
X-RAY DIFFRACTIONr_scangle_it6.0114.5684
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 65 -
Rwork0.23 1254 -
all-1319 -
obs--100 %

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