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- PDB-5m35: The molecular tweezer CLR01 stabilizes a disordered protein-prote... -

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Basic information

Entry
Database: PDB / ID: 5m35
TitleThe molecular tweezer CLR01 stabilizes a disordered protein-protein interface
Components
  • (M-phase inducer phosphatase ...) x 2
  • 14-3-3 protein zeta/delta
KeywordsHYDROLASE / Stabilization / 14-3-3 / disordered PPI interface / CDC25C
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / Golgi reassembly / synaptic target recognition / WW domain binding / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / tube formation / Rap1 signalling ...positive regulation of G2/MI transition of meiotic cell cycle / Golgi reassembly / synaptic target recognition / WW domain binding / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / tube formation / Rap1 signalling / Polo-like kinase mediated events / negative regulation of protein localization to nucleus / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / KSRP (KHSRP) binds and destabilizes mRNA / regulation of mitotic nuclear division / GP1b-IX-V activation signalling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cyclin-dependent protein serine/threonine kinase activity / phosphoprotein phosphatase 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 / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / Cyclin A/B1/B2 associated events during G2/M transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / positive regulation of G2/M transition of mitotic cell cycle / ERK1 and ERK2 cascade / negative regulation of innate immune response / protein sequestering activity / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / regulation of ERK1 and ERK2 cascade / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein tyrosine phosphatase 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 / lung development / regulation of protein stability / mitochondrial intermembrane space / G2/M transition of mitotic cell cycle / melanosome / spermatogenesis / DNA-binding transcription factor binding / angiogenesis / vesicle / cell population proliferation / transmembrane transporter binding / blood microparticle / cadherin binding / protein domain specific binding / cell division / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / 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
M-phase inducer phosphatase / M-phase inducer phosphatase / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / 14-3-3 domain / Rhodanese-like domain superfamily / Rhodanese-like domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...M-phase inducer phosphatase / M-phase inducer phosphatase / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / 14-3-3 domain / Rhodanese-like domain superfamily / Rhodanese-like 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 / M-phase inducer phosphatase 3 / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsBier, D. / Ottmann, C.
Funding support Germany, Netherlands, 3items
OrganizationGrant numberCountry
German Research FoundationCollaborative Research Centre 1093 Germany
Netherlands Organisation for Scientific Research024.001.035 Netherlands
Netherlands Organisation for Scientific Research016.150.366 Netherlands
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface.
Authors: Bier, D. / Mittal, S. / Bravo-Rodriguez, K. / Sowislok, A. / Guillory, X. / Briels, J. / Heid, C. / Bartel, M. / Wettig, B. / Brunsveld, L. / Sanchez-Garcia, E. / Schrader, T. / Ottmann, C.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionNov 15, 2017ID: 5JIT
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Dec 12, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / entity_src_gen / struct_conn
Item: _atom_site.label_alt_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: M-phase inducer phosphatase 3
D: M-phase inducer phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9908
Polymers54,5614
Non-polymers4284
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-26 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.221, 104.075, 114.451
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 26201.566 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 BL21 (bacteria) / References: UniProt: P63104

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M-phase inducer phosphatase ... , 2 types, 2 molecules CD

#2: Protein/peptide M-phase inducer phosphatase 3 / Dual specificity phosphatase Cdc25C


Mass: 1274.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P30307, protein-tyrosine-phosphatase
#3: Protein/peptide M-phase inducer phosphatase 3 / Dual specificity phosphatase Cdc25C


Mass: 883.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P30307, protein-tyrosine-phosphatase

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Non-polymers , 3 types, 123 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


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


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M Ammonium acetate; 0.085 M Sodium citrate pH 5.6; 25.5%(w/v) PEG 4000; 15%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99983 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99983 Å / Relative weight: 1
ReflectionResolution: 2.38→44.85 Å / Num. obs: 35499 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 58.906 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.76
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.38-2.50.5983.110.757199.9
2.5-30.3056.210.973199.9
3-40.07420.950.998199.6
4-60.04235.60.998199.3
6-80.03539.620.999199.3
8-100.0341.850.9991100
10-120.02741.430.999199.6
12-140.02845.010.9981100
14-200.02644.060.9991100
20-400.02642.121197.1
400.03735.981127.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.85 Å
Translation2.5 Å44.85 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NKX

3nkx


Resolution: 2.38→44.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.108 / SU ML: 0.189 / SU R Cruickshank DPI: 0.2523 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.228
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 1746 5 %RANDOM
Rwork0.2243 ---
obs0.2271 33123 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 102.77 Å2 / Biso mean: 55.997 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--3.6 Å20 Å2
3----3.17 Å2
Refinement stepCycle: final / Resolution: 2.38→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 30 119 3804
Biso mean--65.52 58.63 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223765
X-RAY DIFFRACTIONr_bond_other_d0.0160.028
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9815075
X-RAY DIFFRACTIONr_angle_other_deg1.034316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.3465.085469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4125.249181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.12315.044678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051523
X-RAY DIFFRACTIONr_chiral_restr0.1330.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212817
X-RAY DIFFRACTIONr_mcbond_it1.1111.52346
X-RAY DIFFRACTIONr_mcangle_it2.1423736
X-RAY DIFFRACTIONr_scbond_it3.18931419
X-RAY DIFFRACTIONr_scangle_it5.1594.51338
LS refinement shellResolution: 2.381→2.443 Å
RfactorNum. reflection% reflection
Rfree0.45 112 -
Rwork0.337 2126 -
obs--100 %

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