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- PDB-6fbb: Crystal structure of 14-3-3 sigma in complex with wild-type Shroom3 -

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Basic information

Entry
Database: PDB / ID: 6fbb
TitleCrystal structure of 14-3-3 sigma in complex with wild-type Shroom3
Components
  • 14-3-3 protein sigma
  • Shroom3
KeywordsPEPTIDE BINDING PROTEIN / Complex
Function / homology
Function and homology information


cellular pigment accumulation / pattern specification process / apical protein localization / apical junction complex / cortical actin cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / epithelial cell development ...cellular pigment accumulation / pattern specification process / apical protein localization / apical junction complex / cortical actin cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / epithelial cell 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 / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / 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 / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / actin filament organization / adherens junction / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell morphogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / actin filament binding / regulation of cell shape / positive regulation of cell growth / microtubule / cytoskeleton / regulation of cell cycle / cadherin binding / apical plasma membrane / 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
Shroom3 / Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 ...Shroom3 / Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Protein Shroom3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsLeysen, S. / Meijer, F.A. / Milroy, L.G. / Ottmann, C.
CitationJournal: J. Am. Soc. Nephrol. / Year: 2018
Title: Characterization of Coding/Noncoding Variants forSHROOM3in Patients with CKD.
Authors: Prokop, J.W. / Yeo, N.C. / Ottmann, C. / Chhetri, S.B. / Florus, K.L. / Ross, E.J. / Sosonkina, N. / Link, B.A. / Freedman, B.I. / Coppola, C.J. / McDermott-Roe, C. / Leysen, S. / Milroy, L. ...Authors: Prokop, J.W. / Yeo, N.C. / Ottmann, C. / Chhetri, S.B. / Florus, K.L. / Ross, E.J. / Sosonkina, N. / Link, B.A. / Freedman, B.I. / Coppola, C.J. / McDermott-Roe, C. / Leysen, S. / Milroy, L.G. / Meijer, F.A. / Geurts, A.M. / Rauscher, F.J. / Ramaker, R. / Flister, M.J. / Jacob, H.J. / Mendenhall, E.M. / Lazar, J.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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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
P: Shroom3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2766
Polymers27,1562
Non-polymers1204
Water5,477304
1
A: 14-3-3 protein sigma
P: Shroom3
hetero molecules

A: 14-3-3 protein sigma
P: Shroom3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,55212
Polymers54,3134
Non-polymers2398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4430 Å2
ΔGint-80 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.528, 112.241, 62.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

MG

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Components

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


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Nico21 / References: UniProt: P31947
#2: Protein/peptide Shroom3


Mass: 613.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TF72*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.095 M HEPES pH7.3 0.19 M CaCl2 26% PEG400 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.63 Å / Num. obs: 71785 / % possible obs: 100 % / Redundancy: 12.7 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.3→1.32 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.3→45.626 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.68
RfactorNum. reflection% reflection
Rfree0.1664 3513 4.9 %
Rwork0.1541 --
obs0.1547 71757 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→45.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 4 304 2176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082062
X-RAY DIFFRACTIONf_angle_d0.8942806
X-RAY DIFFRACTIONf_dihedral_angle_d17.88837
X-RAY DIFFRACTIONf_chiral_restr0.062311
X-RAY DIFFRACTIONf_plane_restr0.006367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31780.22261510.18242723X-RAY DIFFRACTION100
1.3178-1.33660.19781550.17512692X-RAY DIFFRACTION100
1.3366-1.35660.20631260.16952683X-RAY DIFFRACTION100
1.3566-1.37780.17231180.16622742X-RAY DIFFRACTION100
1.3778-1.40040.20491410.15782705X-RAY DIFFRACTION100
1.4004-1.42450.18031450.15322690X-RAY DIFFRACTION100
1.4245-1.45040.1741280.13762701X-RAY DIFFRACTION100
1.4504-1.47830.1391270.12622720X-RAY DIFFRACTION100
1.4783-1.50850.15361590.12232674X-RAY DIFFRACTION100
1.5085-1.54130.14091480.11992717X-RAY DIFFRACTION100
1.5413-1.57720.15551430.11562709X-RAY DIFFRACTION100
1.5772-1.61660.17391420.11712716X-RAY DIFFRACTION100
1.6166-1.66030.14441350.12562719X-RAY DIFFRACTION100
1.6603-1.70920.16181330.12362708X-RAY DIFFRACTION100
1.7092-1.76440.17751550.13732685X-RAY DIFFRACTION100
1.7644-1.82740.16081380.13852745X-RAY DIFFRACTION100
1.8274-1.90060.16751370.15072715X-RAY DIFFRACTION100
1.9006-1.98710.17351440.14512729X-RAY DIFFRACTION100
1.9871-2.09180.15191440.14472731X-RAY DIFFRACTION100
2.0918-2.22290.15151420.14282736X-RAY DIFFRACTION100
2.2229-2.39450.15431380.14062756X-RAY DIFFRACTION100
2.3945-2.63550.17291390.15332753X-RAY DIFFRACTION100
2.6355-3.01680.18931400.17152778X-RAY DIFFRACTION100
3.0168-3.80050.171450.16512789X-RAY DIFFRACTION100
3.8005-45.65420.1581400.18542928X-RAY DIFFRACTION100

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