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- PDB-5jm4: Crystal structure of 14-3-3zeta in complex with a cyclic peptide ... -

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Basic information

Entry
Database: PDB / ID: 5jm4
TitleCrystal structure of 14-3-3zeta in complex with a cyclic peptide involving an adamantyl and a dicarboxy side chain
Components
  • 14-3-3 protein zeta/delta
  • GLN-GLY-MKD-ANG-ASP-MKD-LEU-ASP-LEU-ALA-CLU
KeywordsSIGNALING PROTEIN / peptidomimetic / PPI inhibitor / macrocycle
Function / homology
Function and homology information


Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / 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 ...Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / 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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / 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 / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / regulation of ERK1 and ERK2 cascade / protein sequestering activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / melanosome / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / cadherin 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 / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsBier, D. / Krueger, D. / Glas, A. / Wallraven, K. / Ottmann, C. / Hennig, S. / Grossmann, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Emmy Noether programGR3592/2-1 Germany
German Research FoundationSFB1093 Germany
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein-Protein Interactions.
Authors: Kruger, D.M. / Glas, A. / Bier, D. / Pospiech, N. / Wallraven, K. / Dietrich, L. / Ottmann, C. / Koch, O. / Hennig, S. / Grossmann, T.N.
History
DepositionApr 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Dec 19, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
D: GLN-GLY-MKD-ANG-ASP-MKD-LEU-ASP-LEU-ALA-CLU
E: GLN-GLY-MKD-ANG-ASP-MKD-LEU-ASP-LEU-ALA-CLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6876
Polymers55,4434
Non-polymers2442
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-10 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.920, 105.740, 113.930
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide GLN-GLY-MKD-ANG-ASP-MKD-LEU-ASP-LEU-ALA-CLU


Mass: 1404.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 4.6 Å3/Da / Density % sol: 73.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.09 M HEPES sodium salt pH 7.5; 1.26 M tri-Sodium citrate; 10 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91909 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91909 Å / Relative weight: 1
ReflectionResolution: 2.34→47.77 Å / Num. obs: 44013 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.52 % / Biso Wilson estimate: 58.028 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.108 / Χ2: 1.032 / Net I/σ(I): 12.52 / Num. measured all: 286758
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.34-2.60.7842.787660611767117660.5980.852100
2.6-30.4415.717611611087110850.9370.478100
3-40.121167864612053120490.9960.131100
4-60.05427.4538614632263080.9980.05999.8
6-80.04230.189826158215790.9990.04699.8
8-100.03332.9531475785750.9990.03799.5
10-120.02835.2815922692680.9990.03199.6
12-140.03335.818461341340.9990.036100
14-200.03334.639441621610.9990.03699.4
20-400.03130.3740884830.9970.03498.8
400.02824.43131650.9980.03231.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.77 Å
Translation2.5 Å47.77 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NKX

3nkx


Resolution: 2.34→47.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.989 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 2196 5 %RANDOM
Rwork0.1981 ---
obs0.2004 41755 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.02 Å2 / Biso mean: 55.691 Å2 / Biso min: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å2-0 Å20 Å2
2---0.15 Å2-0 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 2.34→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 18 103 3830
Biso mean--53.33 56.38 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023797
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.9945121
X-RAY DIFFRACTIONr_angle_other_deg1.861332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09225170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.02215640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7231523
X-RAY DIFFRACTIONr_chiral_restr0.1460.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022789
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 149 -
Rwork0.345 2841 -
all-2990 -
obs--100 %

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