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- PDB-5xy9: Structure of the MST4 and 14-3-3 complex -

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Basic information

Entry
Database: PDB / ID: 5xy9
TitleStructure of the MST4 and 14-3-3 complex
Components
  • 14-3-3 protein zeta/delta
  • Peptide from Serine/threonine-protein kinase 26
KeywordsPROTEIN BINDING / Kinase / Protein Complex / Phosphorylation / Signaling protein / Melanoma metastasis
Function / homology
Function and homology information


microvillus assembly / Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / vesicle membrane / tube formation / Rap1 signalling ...microvillus assembly / Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / vesicle membrane / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / Golgi-associated vesicle / GP1b-IX-V activation signalling / Apoptotic cleavage of cellular proteins / 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 / 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 / cellular response to starvation / hippocampal mossy fiber to CA3 synapse / negative regulation of cell migration / regulation of ERK1 and ERK2 cascade / cell periphery / 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 / melanosome / cellular response to oxidative stress / regulation of apoptotic process / angiogenesis / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / protein autophosphorylation / blood microparticle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / apical plasma membrane / protein domain specific binding / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
MST4, kinase domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation 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 ...MST4, kinase domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation 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 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Serine/threonine-protein kinase 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsShi, Z.B. / Zhou, Z.C.
CitationJournal: To Be Published
Title: Structure of the MST4 and 14-3-3 complex
Authors: Shi, Z. / Zhou, Z.
History
DepositionJul 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Peptide from Serine/threonine-protein kinase 26
D: Peptide from Serine/threonine-protein kinase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4146
Polymers63,9674
Non-polymers4472
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-15 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.994, 84.734, 111.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 30444.102 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(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPLus / References: UniProt: P63104
#2: Protein/peptide Peptide from Serine/threonine-protein kinase 26 / MST3 and SOK1-related kinase / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / ...MST3 and SOK1-related kinase / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / Serine/threonine-protein kinase MASK


Mass: 1539.457 Da / Num. of mol.: 2 / Fragment: UNP residues 314-325 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9P289, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 31310 / % possible obs: 99.9 % / Redundancy: 14 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 38
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 3 / Num. unique obs: 1527 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJA

1qja


Resolution: 2.303→34.821 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 1999 6.4 %
Rwork0.1953 --
obs0.1985 31225 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→34.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 23 94 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073817
X-RAY DIFFRACTIONf_angle_d0.9165159
X-RAY DIFFRACTIONf_dihedral_angle_d6.6913182
X-RAY DIFFRACTIONf_chiral_restr0.053582
X-RAY DIFFRACTIONf_plane_restr0.005671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3033-2.36090.37481370.31111991X-RAY DIFFRACTION96
2.3609-2.42470.37181390.28782063X-RAY DIFFRACTION100
2.4247-2.4960.3241400.26482036X-RAY DIFFRACTION100
2.496-2.57660.32751410.24212067X-RAY DIFFRACTION100
2.5766-2.66860.32491420.22772074X-RAY DIFFRACTION100
2.6686-2.77540.29151410.2392073X-RAY DIFFRACTION100
2.7754-2.90170.31011430.23182077X-RAY DIFFRACTION100
2.9017-3.05460.27731420.23282085X-RAY DIFFRACTION100
3.0546-3.24580.26551430.21922075X-RAY DIFFRACTION100
3.2458-3.49620.24721430.20412103X-RAY DIFFRACTION100
3.4962-3.84770.21691450.18162114X-RAY DIFFRACTION100
3.8477-4.40350.18271440.14772104X-RAY DIFFRACTION100
4.4035-5.54430.23711460.16032134X-RAY DIFFRACTION100
5.5443-34.82540.20471530.18032230X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.20642.54013.79832.8542-1.01643.98640.0729-0.94490.09570.60.22620.0612-0.5807-0.929-0.14240.68170.2620.11650.8155-0.02050.494739.636610.610114.1588
22.2538-0.18392.48691.31061.90878.2798-0.13720.15920.1585-0.129-0.0444-0.0654-0.22880.44270.18180.44690.03660.04560.37870.06830.359749.0236.2072-5.0234
35.1904-1.62851.68014.2393-0.6566.4662-0.1318-0.16890.25020.35490.0885-0.2623-0.73850.71570.02580.3678-0.01940.00580.3671-0.05610.32960.62484.60339.534
44.53022.3890.07157.3993-2.46794.3538-0.0022-0.0458-0.19610.26270.096-0.0771-0.0823-0.1336-0.06530.27260.0637-0.01580.4605-0.05010.297159.0239-11.94410.6043
54.593-0.699-0.01882.06090.34055.75190.00920.1412-0.0302-0.14890.10810.3067-0.043-0.4847-0.16080.48270.1315-0.01520.38250.05010.502129.78045.9937-11.7788
63.39020.32531.87071.88010.37755.1847-0.3407-0.8920.22910.17580.170.377-0.853-1.07470.1340.52780.22730.03850.56270.01910.609221.43212.2504-1.9432
71.25430.49881.03124.00580.36882.2039-0.08960.13960.3282-0.0616-0.03290.5132-0.1425-0.65070.15040.32130.10120.02560.7322-0.00880.619111.9122-4.9233-11.8819
88.6-2.6751-1.08368.26422.4996.5776-0.02280.8739-1.33840.1696-0.13271.75850.60890.10010.43170.6890.09370.05830.6703-0.07660.622250.6443-6.82073.4595
92.24130.29324.06467.6178-1.46278.08290.26750.1349-0.6850.80080.1177-1.1636-0.04640.8562-0.40240.69630.0492-0.06310.99330.0260.857221.1273-5.7655-5.199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 230 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 111 )
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 230 )
8X-RAY DIFFRACTION8chain 'C' and (resid 316 through 325 )
9X-RAY DIFFRACTION9chain 'D' and (resid 316 through 325 )

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