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- PDB-4n7g: Crystal structure of 14-3-3zeta in complex with a peptide derived... -

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Basic information

Entry
Database: PDB / ID: 4n7g
TitleCrystal structure of 14-3-3zeta in complex with a peptide derived from ExoS
Components
  • 14-3-3 protein zeta/delta
  • Exoenzyme S
KeywordsSIGNALING PROTEIN / 14-3-3 / adaptor protein / protein-protein interaction / cross-link
Function / homology
Function and homology information


synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / glycosyltransferase activity / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / nucleotidyltransferase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / GTPase activator activity / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / intracellular protein localization / melanosome / toxin activity / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / protein phosphorylation / cadherin binding / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 ...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
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: 2.25 Å
AuthorsBier, D. / Glas, A. / Hahne, G. / Grossmann, T. / Ottmann, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Constrained peptides with target-adapted cross-links as inhibitors of a pathogenic protein-protein interaction.
Authors: Glas, A. / Bier, D. / Hahne, G. / Rademacher, C. / Ottmann, C. / Grossmann, T.N.
History
DepositionOct 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Exoenzyme S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2477
Polymers27,8352
Non-polymers1,4125
Water1,11762
1
A: 14-3-3 protein zeta/delta
B: Exoenzyme S
hetero molecules

A: 14-3-3 protein zeta/delta
B: Exoenzyme S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49414
Polymers55,6714
Non-polymers2,82310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8210 Å2
ΔGint-18 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.420, 105.420, 114.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 26720.217 Da / Num. of mol.: 1 / Fragment: UNP residues 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP_001129171.1, YWHAZ / Plasmid: pProEx HTb / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P63104
#2: Protein/peptide Exoenzyme S


Mass: 1115.236 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 420-430) / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q93SQ3
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 6.59 Å3/Da / Density % sol: 81.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M sodium chloride, 0.1 M sodium acetate, pH 4.5, 40% v/v PEG300, VAPOR DIFFUSION, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.44 Å / Num. all: 35325 / Num. obs: 35293 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.941 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 19.69
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.34.46335662203100
2.3-2.355.35323592045100
2.35-2.46.1131839187399.9
2.4-2.68.71059496137100
2.6-2.812.85766784512100
2.8-316.51545263430100
3-530.9519289711726100
5-738.33339692118100
7-939.069037654100
9-1241.755313354100
1239.97372227396.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.44 Å
Translation2.5 Å48.44 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2289 / WRfactor Rwork: 0.1951 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.8661 / SU B: 3.125 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1243 / SU Rfree: 0.1272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1766 5 %RANDOM
Rwork0.1887 ---
obs0.1904 35293 99.97 %-
all-35325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.61 Å2 / Biso mean: 47.3521 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å2-0 Å2
2--0.84 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 95 62 2060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022033
X-RAY DIFFRACTIONr_angle_refined_deg2.6442.0112697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.885239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44525.57995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7851511
X-RAY DIFFRACTIONr_chiral_restr0.2160.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021439
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 121 -
Rwork0.242 2277 -
all-2398 -
obs--100 %

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