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- PDB-5wfx: Structural basis for the interaction of 14-3-3beta with Tricarbox... -

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Basic information

Entry
Database: PDB / ID: 5wfx
TitleStructural basis for the interaction of 14-3-3beta with Tricarboxylic Acid Cycle intermediate Malate
Components14-3-3 protein beta/alpha
KeywordsPROTEIN TRANSPORT / ChREBP / transcription activation
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Regulation of localization of FOXO transcription factors / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo / Negative regulation of MAPK pathway ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Regulation of localization of FOXO transcription factors / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo / Negative regulation of MAPK pathway / TP53 Regulates Metabolic Genes / RAF activation / mTORC1-mediated signalling / negative regulation of protein dephosphorylation / MAP2K and MAPK activation / cytoplasmic sequestering of protein / Rap1 signalling / negative regulation of G protein-coupled receptor signaling pathway / protein kinase inhibitor activity / phosphoserine residue binding / protein targeting / transcription repressor complex / phosphoprotein binding / intracellular protein transport / histone deacetylase binding / melanosome / protein domain specific binding / negative regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / protein-containing complex / identical protein binding / 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
14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsHou, Z.Q.
CitationJournal: To Be Published
Title: Structural basis for the interaction of 14-3-3 beta withTricarboxylic Acid Cycle intermediate Malate
Authors: Hou, Z.Q. / Su, L.J. / Liu, X.Y.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Assembly

Deposited unit
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha


Theoretical massNumber of molelcules
Total (without water)56,2372
Polymers56,2372
Non-polymers00
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-11 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.930, 87.790, 124.044
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 beta/alpha / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28118.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ywhab / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: 2.2M Sodium Malonate pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 78578 / % possible obs: 99.3 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.3

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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: 5WFU

5wfu


Resolution: 1.651→38.687 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77
RfactorNum. reflection% reflection
Rfree0.2308 3583 5.04 %
Rwork0.2001 --
obs0.2016 71071 89.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.651→38.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 0 654 4335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063731
X-RAY DIFFRACTIONf_angle_d0.8045028
X-RAY DIFFRACTIONf_dihedral_angle_d2.4222314
X-RAY DIFFRACTIONf_chiral_restr0.041566
X-RAY DIFFRACTIONf_plane_restr0.004651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6507-1.67240.3398600.257854X-RAY DIFFRACTION31
1.6724-1.69530.2605600.24671186X-RAY DIFFRACTION41
1.6953-1.71950.2027780.24951644X-RAY DIFFRACTION56
1.7195-1.74520.2961120.25771904X-RAY DIFFRACTION67
1.7452-1.77240.32811050.23742165X-RAY DIFFRACTION75
1.7724-1.80150.31771290.2252295X-RAY DIFFRACTION81
1.8015-1.83260.3011460.22642504X-RAY DIFFRACTION87
1.8326-1.86590.251390.22382663X-RAY DIFFRACTION93
1.8659-1.90180.23791450.23152767X-RAY DIFFRACTION97
1.9018-1.94060.31961720.24432831X-RAY DIFFRACTION99
1.9406-1.98280.27531480.21532840X-RAY DIFFRACTION100
1.9828-2.02890.23611520.19872880X-RAY DIFFRACTION100
2.0289-2.07960.21421540.18932880X-RAY DIFFRACTION100
2.0796-2.13590.20731380.18862875X-RAY DIFFRACTION100
2.1359-2.19870.21651530.18582892X-RAY DIFFRACTION100
2.1987-2.26970.24391610.19462886X-RAY DIFFRACTION100
2.2697-2.35080.21221530.19092871X-RAY DIFFRACTION100
2.3508-2.44490.24131460.18982886X-RAY DIFFRACTION100
2.4449-2.55610.22571580.19672907X-RAY DIFFRACTION100
2.5561-2.69090.22851610.20192897X-RAY DIFFRACTION100
2.6909-2.85940.23671380.20612959X-RAY DIFFRACTION100
2.8594-3.08010.24561560.20612899X-RAY DIFFRACTION100
3.0801-3.38990.23461420.19382954X-RAY DIFFRACTION100
3.3899-3.880.18771460.16662947X-RAY DIFFRACTION100
3.88-4.88690.18021570.16122996X-RAY DIFFRACTION100
4.8869-38.69770.22051740.23613106X-RAY DIFFRACTION100

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