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- PDB-6a5q: Structure of 14-3-3 beta in complex with TFEB 14-3-3 binding motif -

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Basic information

Entry
Database: PDB / ID: 6a5q
TitleStructure of 14-3-3 beta in complex with TFEB 14-3-3 binding motif
Components
  • 14-3-3 protein beta/alpha
  • TFEB pS211-peptide
KeywordsTRANSCRIPTION / PHOSPHOSERIN / REGULATION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling ...negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / Frs2-mediated activation / protein kinase inhibitor activity / positive regulation of catalytic activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Negative regulation of MAPK pathway / histone deacetylase binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / melanosome / Signaling by BRAF and RAF1 fusions / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / membrane / 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
MALONIC ACID / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, Y. / Ren, J.Q. / Feng, W.
CitationJournal: Autophagy / Year: 2019
Title: YWHA/14-3-3 proteins recognize phosphorylated TFEB by a noncanonical mode for controlling TFEB cytoplasmic localization.
Authors: Xu, Y. / Ren, J. / He, X. / Chen, H. / Wei, T. / Feng, W.
History
DepositionJun 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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
B: 14-3-3 protein beta/alpha
A: 14-3-3 protein beta/alpha
C: 14-3-3 protein beta/alpha
D: TFEB pS211-peptide
E: TFEB pS211-peptide
F: TFEB pS211-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2239
Polymers89,9116
Non-polymers3123
Water7,819434
1
B: 14-3-3 protein beta/alpha
A: 14-3-3 protein beta/alpha
E: TFEB pS211-peptide
F: TFEB pS211-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1496
Polymers59,9414
Non-polymers2082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-46 kcal/mol
Surface area22620 Å2
MethodPISA
2
C: 14-3-3 protein beta/alpha
D: TFEB pS211-peptide
hetero molecules

C: 14-3-3 protein beta/alpha
D: TFEB pS211-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1496
Polymers59,9414
Non-polymers2082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area5940 Å2
ΔGint-47 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.170, 85.170, 209.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28412.672 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P31946
#2: Protein/peptide TFEB pS211-peptide


Mass: 1557.616 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4 / Details: 0.1 M sodium malonate, and 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 60151 / % possible obs: 99.5 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 24.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 5860 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQ0

2bq0


Resolution: 2→36.88 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.54
RfactorNum. reflection% reflection
Rfree0.2295 2002 3.33 %
Rwork0.1857 --
obs0.1871 60079 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.84 Å2 / Biso mean: 30.2336 Å2 / Biso min: 11.88 Å2
Refinement stepCycle: final / Resolution: 2→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5789 0 21 434 6244
Biso mean--35.5 38.03 -
Num. residues----727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075930
X-RAY DIFFRACTIONf_angle_d0.8058010
X-RAY DIFFRACTIONf_chiral_restr0.044896
X-RAY DIFFRACTIONf_plane_restr0.0051046
X-RAY DIFFRACTIONf_dihedral_angle_d2.6165115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0005-2.05050.28911400.223404599
2.0505-2.10590.25891430.2089406299
2.1059-2.16790.26151370.194406499
2.1679-2.23790.24031400.1896410699
2.2379-2.31780.24331450.1845404499
2.3178-2.41060.25431390.1857411999
2.4106-2.52030.24261380.1815410299
2.5203-2.65320.23331440.19054150100
2.6532-2.81930.24341400.18624140100
2.8193-3.03690.22821460.19414151100
3.0369-3.34240.2211440.18734174100
3.3424-3.82560.22581420.18344221100
3.8256-4.81810.22181470.16484256100
4.81810.1991570.19014443100

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