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- PDB-4n84: Crystal structure of 14-3-3zeta in complex with a 12-carbon-linke... -

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Basic information

Entry
Database: PDB / ID: 4n84
TitleCrystal structure of 14-3-3zeta in complex with a 12-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 / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / 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 / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / 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 / 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 / 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 / negative regulation of innate immune response / ERK1 and ERK2 cascade / 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 / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / protein localization / melanosome / toxin activity / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / cadherin binding / protein phosphorylation / protein domain specific binding / 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: 2.5 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 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Exoenzyme S
E: Exoenzyme S


Theoretical massNumber of molelcules
Total (without water)54,7484
Polymers54,7484
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-19 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.240, 105.180, 113.780
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: 26260.656 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: 1113.347 Da / Num. of mol.: 2 / Fragment: modified peptide (UNP residues 421-430) / Mutation: L422(MKD),A425(MKD) / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q93SQ3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.55 Å3/Da / Density % sol: 72.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 8
Details: 1 M potassium sodium tartrate, 0.1 M sodium chloride, 0.1 M imidazole, pH 8.0, cryoprotectant: 20% 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: Jul 13, 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: 2.5→47.74 Å / Num. all: 35305 / Num. obs: 35246 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.858 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.60.7734.16483963865100
2.6-30.3539.1414743810802100
3-40.10422.7614800711740100
4-60.0635.85768866155100
6-80.0536.1217105154099.7
8-100.03942.99698256199.8
10-120.04242.983248266100
120.04139.99408937697.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.74 Å
Translation2.5 Å47.74 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: 2.5→47.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2488 / WRfactor Rwork: 0.2046 / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.8212 / SU B: 6.583 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2333 / SU Rfree: 0.2128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1764 5 %RANDOM
Rwork0.2022 ---
obs0.2045 35246 99.96 %-
all-35305 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.7 Å2 / Biso mean: 54.4754 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0 Å20 Å2
2--0.39 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 0 42 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023771
X-RAY DIFFRACTIONr_angle_refined_deg2.1661.9825061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14425.47181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36115701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3861522
X-RAY DIFFRACTIONr_chiral_restr0.1550.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022758
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 117 -
Rwork0.387 2269 -
all-2386 -
obs--100 %

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