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- PDB-5m36: The molecular tweezer CLR01 stabilizes a disordered protein-prote... -

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Basic information

Entry
Database: PDB / ID: 5m36
TitleThe molecular tweezer CLR01 stabilizes a disordered protein-protein interface
Components
  • 14-3-3 protein zeta/delta
  • M-phase inducer phosphatase 3
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 / 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 / Polo-like kinase mediated events ...positive regulation of G2/MI transition of meiotic cell cycle / 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 / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / KSRP (KHSRP) binds and destabilizes mRNA / regulation of mitotic nuclear division / WW domain binding / GP1b-IX-V activation signalling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / 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 / 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 / Activation of ATR in response to replication stress / Cyclin A/B1/B2 associated events during G2/M transition / cellular response to glucose starvation / 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 / protein tyrosine phosphatase activity / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / protein-tyrosine-phosphatase / non-membrane spanning protein tyrosine phosphatase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / mitochondrial intermembrane space / G2/M transition of mitotic cell cycle / intracellular protein localization / melanosome / angiogenesis / DNA-binding transcription factor binding / spermatogenesis / vesicle / blood microparticle / transmembrane transporter binding / cell population proliferation / nuclear speck / protein phosphorylation / cadherin binding / protein domain specific binding / cell division / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / 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. / Rhodanese-like domain superfamily / Rhodanese-like domain / 14-3-3 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. / Rhodanese-like domain superfamily / Rhodanese-like domain / 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
Chem-9SZ / 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: 2.45 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: 5JIV
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 1.2Dec 12, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.4Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)64,98513
Polymers61,5584
Non-polymers3,4279
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-23 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.520, 102.360, 112.820
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 / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 4577.229 Da / Num. of mol.: 2 / Mutation: UNP residues 207-244 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P30307, protein-tyrosine-phosphatase

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Non-polymers , 4 types, 76 molecules

#3: Chemical
ChemComp-9SZ / (1R,5S,9S,16R,20R,24S,28S,35R)-3,22-Bis(dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaene


Mass: 726.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H32O8P2
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.7 Å3/Da / Density % sol: 66.72 %
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: 0.989 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: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.45→46.61 Å / Num. obs: 31166 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.066 % / Biso Wilson estimate: 68.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Χ2: 1.023 / Net I/σ(I): 26.68 / Num. measured all: 407229 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.613.0140.9233.164888499649860.9590.96199.8
2.6-313.7210.3757.26123257899189830.9910.3999.9
3-413.1810.07129.5128938978597820.9990.073100
4-612.4550.03459.61638305127512510.036100
6-812.1160.0365.34155931288128710.03299.9
8-1010.4340.02470.73483146346310.025100
10-1211.4080.02476.13254422422310.02599.6
12-1411.460.02775.7129511311310.028100
14-2011.1090.02576.74143312912910.026100
20-46.618.2670.02859.84620857510.0388.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.61 Å
Translation2.5 Å46.61 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PHASER2.3.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NKX

3nkx


Resolution: 2.45→46.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2737 / WRfactor Rwork: 0.2222 / FOM work R set: 0.6936 / SU B: 13.025 / SU ML: 0.267 / SU R Cruickshank DPI: 0.3039 / SU Rfree: 0.2512 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1555 5 %RANDOM
Rwork0.2238 ---
obs0.2264 29554 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.5 Å2 / Biso mean: 77.665 Å2 / Biso min: 47.11 Å2
Baniso -1Baniso -2Baniso -3
1--6.4 Å2-0 Å2-0 Å2
2--8.89 Å20 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 2.45→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 244 67 3990
Biso mean--127.1 72.59 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024039
X-RAY DIFFRACTIONr_bond_other_d0.0020.023561
X-RAY DIFFRACTIONr_angle_refined_deg1.3762.0025527
X-RAY DIFFRACTIONr_angle_other_deg1.2143.018263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92224.809183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34615670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0451527
X-RAY DIFFRACTIONr_chiral_restr0.0740.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 112 -
Rwork0.377 2147 -
all-2259 -
obs--99.87 %

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