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- PDB-5j31: Crystal structure of 14-3-3zeta in complex with an alkyne cross-l... -

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Basic information

Entry
Database: PDB / ID: 5j31
TitleCrystal structure of 14-3-3zeta in complex with an alkyne cross-linked cyclic peptide derived from ExoS
Components
  • 14-3-3 protein zeta/delta
  • Exoenzyme S
KeywordsSIGNALING PROTEIN / constrained peptides / protein-protein-interaction / alkyne cross-link / 14-3-3 protein zeta
Function / homology
Function and homology information


Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / NAD+-protein poly-ADP-ribosyltransferase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / nucleotidyltransferase activity / GTPase activator activity / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / lung development / regulation of protein stability / melanosome / toxin activity / angiogenesis / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / blood microparticle / cadherin binding / protein domain specific binding / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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
BENZOIC ACID / 14-3-3 protein zeta/delta / Exoenzyme S
Similarity search - Component
Biological speciesHomo sapiens (human)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsWallraven, K. / Cromm, P. / Bier, D. / Glas, A. / Grossmann, T.
CitationJournal: Chembiochem / Year: 2016
Title: Constraining an Irregular Peptide Secondary Structure through Ring-Closing Alkyne Metathesis.
Authors: Cromm, P.M. / Wallraven, K. / Glas, A. / Bier, D. / Furstner, A. / Ottmann, C. / Grossmann, T.N.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Exoenzyme S
D: Exoenzyme S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9745
Polymers54,8524
Non-polymers1221
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-19 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.940, 105.580, 114.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pProEx HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P63104
#2: Protein/peptide Exoenzyme S


Mass: 1109.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q93SQ3
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 4.68 Å3/Da / Density % sol: 73.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1.26 M Tri-Sodium Citrate, 0.09 M HEPES pH 7.5, 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.94 Å / Num. obs: 40511 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.28 % / Biso Wilson estimate: 62.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.54
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.613.790.5085.881100
2.6-313.270.21112.431100
3-413.40.05736.631100
4-612.960.03461.44199.9
6-812.790.03565.131100
8-1011.280.03169.41199.7
10-125.050.03268.621100
12-1412.440.03174.111100
14-2013.770.03172.441100
20-4010.060.03265.721100
407.170.02755.31137.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.82 Å47.94 Å
Translation5.82 Å47.94 Å

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Processing

Software
NameVersionClassification
XSCALE2015data scaling
PHASER2.5.1phasing
REFMAC2.5.1refinement
PDB_EXTRACT3.2data extraction
XDS2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FJ3

4fj3


Resolution: 2.4→47.94 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.801 / SU ML: 0.129 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.176
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2025 5 %RANDOM
Rwork0.1631 ---
obs0.1659 38425 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.06 Å2 / Biso mean: 65.535 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-6.09 Å20 Å2-0 Å2
2---2.03 Å20 Å2
3----4.07 Å2
Refinement stepCycle: final / Resolution: 2.4→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 9 358 4193
Biso mean--46.98 70.08 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023877
X-RAY DIFFRACTIONr_bond_other_d0.010.023766
X-RAY DIFFRACTIONr_angle_refined_deg3.3871.9895202
X-RAY DIFFRACTIONr_angle_other_deg1.3053.0058679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27625.532188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26915747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211522
X-RAY DIFFRACTIONr_chiral_restr0.1410.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
LS refinement shellResolution: 2.4→2.462 Å
RfactorNum. reflection% reflection
Rfree0.274 147 5 %
Rwork0.254 2789 -
obs--100 %

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