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- PDB-4n7y: Crystal structure of 14-3-3zeta in complex with a 8-carbon-linker... -

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Basic information

Entry
Database: PDB / ID: 4n7y
TitleCrystal structure of 14-3-3zeta in complex with a 8-carbon-linker cyclic 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


Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / regulation of synapse maturation / 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 / establishment of Golgi localization / regulation of synapse maturation / 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 / NAD+-protein poly-ADP-ribosyltransferase activity / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / 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 / nucleotidyltransferase activity / hippocampal mossy fiber to CA3 synapse / 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 / protein localization / 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 / 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: 2.16 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 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)55,8114
Polymers55,8114
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-20 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.510, 103.520, 114.040
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: 26720.217 Da / Num. of mol.: 2 / 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: 1185.368 Da / Num. of mol.: 2 / Fragment: modified peptide (UNP residues 420-430) / Mutation: L422(2JN),A425(MK8) / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q93SQ3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.09 M HEPES sodium, pH 7.5, 1.26 M sodium citrate, 10% v/v glycerol, 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: Feb 23, 2013
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: 2.16→49.94 Å / Num. all: 46830 / Num. obs: 46765 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 54.78 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.16-2.180.9432.61156731271100
2.18-2.20.83.2116503122799.9
2.2-2.50.4086.3518257713896100
2.5-2.60.22211.38457873315100
2.6-2.80.15615.87725875323100
2.8-30.11321.35511193980100
3-40.06733.8912854510125100
4-60.05240.78632035317100
6-80.04541.08157161332100
8-100.03641.345382491100
10-120.03944.862779222100
12-150.03743.621866157100
15-200.0442.71108896100
200.03837.287457889.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.05 Å
Translation2.5 Å47.05 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: 2.16→49.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2675 / WRfactor Rwork: 0.2238 / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.8302 / SU B: 4.134 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1672 / SU Rfree: 0.1637 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2340 5 %RANDOM
Rwork0.2127 ---
obs0.2149 46765 99.98 %-
all-46830 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.37 Å2 / Biso mean: 50.8219 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20 Å2
2--2.08 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.16→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 0 45 3774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023752
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9815042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01425.449178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6931521
X-RAY DIFFRACTIONr_chiral_restr0.2230.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022745
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 153 -
Rwork0.31 3026 -
all-3179 -
obs--99.97 %

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