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- PDB-6qiu: Crystal structure of 14-3-3 sigma in complex with Ataxin-1 Ser776... -

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Basic information

Entry
Database: PDB / ID: 6qiu
TitleCrystal structure of 14-3-3 sigma in complex with Ataxin-1 Ser776 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Ataxin-1 phosphopeptide
KeywordsPROTEIN BINDING / phosphoprotein binding anti-aggregation
Function / homology
Function and homology information


poly(G) binding / negative regulation of insulin-like growth factor receptor signaling pathway / POZ domain binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / lung alveolus development / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation ...poly(G) binding / negative regulation of insulin-like growth factor receptor signaling pathway / POZ domain binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / lung alveolus development / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / positive regulation of glial cell proliferation / social behavior / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / RNA processing / 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 / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / insulin-like growth factor receptor signaling pathway / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / adult locomotory behavior / positive regulation of protein export from nucleus / stem cell proliferation / excitatory postsynaptic potential / learning / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / brain development / visual learning / memory / nuclear matrix / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / transcription by RNA polymerase II / postsynapse / regulation of cell cycle / cadherin binding / negative regulation of DNA-templated transcription / chromatin binding / protein kinase binding / nucleolus / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ataxin-1, N-terminal / ATAXIN1-like / Ataxin-1 like family / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / 14-3-3 domain / Delta-Endotoxin; domain 1 ...Ataxin-1, N-terminal / ATAXIN1-like / Ataxin-1 like family / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 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 sigma / Ataxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.802 Å
AuthorsLeysen, S. / Milroy, L.G. / Davis, J.M. / Brunsveld, L. / Ottmann, C.
CitationJournal: To Be Published
Title: Structural insights into the cytoplasmic chaperone effect of 14-3-3 proteins on Ataxin-1
Authors: Leysen, S. / Burnley, R.J. / Rodriguez, E. / Milroy, L.G. / Soini, L. / Adamski, C.J. / Davis, R. / Obsil, T. / Brunsveld, L. / Crabbe, T. / Zoghbi, H.Y. / Ottmann, C. / Davis, J.M.
History
DepositionJan 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Ataxin-1 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9594
Polymers27,8992
Non-polymers602
Water7,782432
1
A: 14-3-3 protein sigma
P: Ataxin-1 phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
P: Ataxin-1 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9188
Polymers55,7994
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5630 Å2
ΔGint-53 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.662, 111.948, 62.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Ataxin-1 phosphopeptide


Mass: 1356.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P54253*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.095 M Hepes (pH 7.1, 7.3, 7.5, 7.7), 0.19 M CaCl2, 5% glycerol, 24-29% PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→45.64 Å / Num. obs: 26519 / % possible obs: 97.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 34.2 / Num. measured all: 169812
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.844.90.216674213760.9650.1040.2417.285.8
9.01-45.645.10.014130625810.0060.015106.898.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.7data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.802→41.768 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 1306 4.93 %
Rwork0.1472 25198 -
obs0.1495 26504 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.01 Å2 / Biso mean: 15.1802 Å2 / Biso min: 2.08 Å2
Refinement stepCycle: final / Resolution: 1.802→41.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 2 432 2383
Biso mean--14.59 26.9 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8021-1.87420.2451370.18012503264088
1.8742-1.95950.211260.15372633275993
1.9595-2.06280.18631330.14492725285896
2.0628-2.19210.18431280.13892827295599
2.1921-2.36130.20721570.141828583015100
2.3613-2.59890.17441420.148928823024100
2.5989-2.97490.19811700.151428543024100
2.9749-3.74770.1741530.135229173070100
3.7477-41.77940.19921600.15222999315999

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