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- PDB-6a5s: Structure of 14-3-3 gamma in complex with TFEB 14-3-3 binding motif -

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Basic information

Entry
Database: PDB / ID: 6a5s
TitleStructure of 14-3-3 gamma in complex with TFEB 14-3-3 binding motif
Components
  • 14-3-3 protein gamma
  • TFEB pS211-peptide
KeywordsTRANSCRIPTION / PHOSPHOSERIN / REGULATION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / insulin-like growth factor receptor binding / Transcriptional and post-translational regulation of MITF-M expression and activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein kinase C binding / protein sequestering activity / AURKA Activation by TPX2 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / receptor tyrosine kinase binding / regulation of synaptic plasticity / positive regulation of T cell activation / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / presynapse / regulation of protein localization / mitochondrial matrix / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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 2.0Feb 27, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _struct.title
Revision 2.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein gamma
E: TFEB pS211-peptide
B: 14-3-3 protein gamma
C: TFEB pS211-peptide
D: 14-3-3 protein gamma
F: TFEB pS211-peptide
G: 14-3-3 protein gamma
H: TFEB pS211-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,97210
Polymers119,9258
Non-polymers472
Water14,466803
1
A: 14-3-3 protein gamma
E: TFEB pS211-peptide
B: 14-3-3 protein gamma
C: TFEB pS211-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0106
Polymers59,9634
Non-polymers472
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-59 kcal/mol
Surface area22930 Å2
MethodPISA
2
D: 14-3-3 protein gamma
F: TFEB pS211-peptide
G: 14-3-3 protein gamma
H: TFEB pS211-peptide


Theoretical massNumber of molelcules
Total (without water)59,9634
Polymers59,9634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-42 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.088, 82.229, 88.092
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28423.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61981
#2: Protein/peptide
TFEB pS211-peptide


Mass: 1557.616 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 803 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.3
Details: 0.1 M Tris-HCl, 0.2 M calcium acetate, and 20% (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 315 / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 73457 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 13.1
Reflection shellResolution: 2.099→2.14 Å / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3618 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UZD

3uzd


Resolution: 2.099→44.044 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.227 2022 2.76 %
Rwork0.1797 --
obs0.181 73368 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.08 Å2 / Biso mean: 25.3333 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 2.099→44.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 2 803 8563
Biso mean--39.46 31.6 -
Num. residues----964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077926
X-RAY DIFFRACTIONf_angle_d0.87510720
X-RAY DIFFRACTIONf_chiral_restr0.0361213
X-RAY DIFFRACTIONf_plane_restr0.0041378
X-RAY DIFFRACTIONf_dihedral_angle_d14.6683034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0994-2.15190.27331410.225041518299
2.1519-2.21010.27811460.210250135159100
2.2101-2.27510.25211660.207950915257100
2.2751-2.34860.2491340.195850805214100
2.3486-2.43250.24651410.187350965237100
2.4325-2.52990.25781520.189650855237100
2.5299-2.6450.26471260.187950865212100
2.645-2.78440.26941600.185550605220100
2.7844-2.95890.23761390.185151165255100
2.9589-3.18720.27921360.183851325268100
3.1872-3.50790.22261710.173650495220100
3.5079-4.01520.19851290.157351615290100
4.0152-5.05750.16721460.152750975243100
5.0575-44.05360.18251350.17745239537499

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