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- PDB-5my9: Crystal structure of human 14-3-3 sigma in complex with LRRK2 pep... -

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Basic information

Entry
Database: PDB / ID: 5my9
TitleCrystal structure of human 14-3-3 sigma in complex with LRRK2 peptide pS935
Components
  • 14-3-3 protein sigma
  • Leucine-rich repeat serine/threonine-protein kinase 2
KeywordsTRANSFERASE / 14-3-3 LRRK2 phosphorylation PPI
Function / homology
Function and homology information


caveola neck / negative regulation of protein processing involved in protein targeting to mitochondrion / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / Wnt signalosome assembly / regulation of cell projection organization / tangential migration from the subventricular zone to the olfactory bulb / GTP-dependent protein kinase activity / regulation of SNARE complex assembly ...caveola neck / negative regulation of protein processing involved in protein targeting to mitochondrion / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / Wnt signalosome assembly / regulation of cell projection organization / tangential migration from the subventricular zone to the olfactory bulb / GTP-dependent protein kinase activity / regulation of SNARE complex assembly / regulation of neuroblast proliferation / regulation of ER to Golgi vesicle-mediated transport / protein localization to endoplasmic reticulum exit site / peroxidase inhibitor activity / negative regulation of late endosome to lysosome transport / regulation of mitochondrial depolarization / negative regulation of protein targeting to mitochondrion / positive regulation of dopamine receptor signaling pathway / amphisome / regulation of synaptic vesicle transport / regulation of CAMKK-AMPK signaling cascade / regulation of lysosomal lumen pH / co-receptor binding / negative regulation of GTPase activity / regulation of neuron maturation / regulation of dopamine receptor signaling pathway / positive regulation of microglial cell activation / regulation of retrograde transport, endosome to Golgi / positive regulation of synaptic vesicle endocytosis / cytoplasmic side of mitochondrial outer membrane / negative regulation of excitatory postsynaptic potential / negative regulation of autophagosome assembly / JUN kinase kinase kinase activity / olfactory bulb development / neuron projection arborization / striatum development / multivesicular body, internal vesicle / regulation of dendritic spine morphogenesis / mitochondrion localization / protein localization to mitochondrion / cellular response to dopamine / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of protein autoubiquitination / endoplasmic reticulum organization / Wnt signalosome / negative regulation of protein processing / positive regulation of programmed cell death / GTP metabolic process / regulation of canonical Wnt signaling pathway / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / lysosome organization / Golgi-associated vesicle / clathrin binding / PTK6 promotes HIF1A stabilization / negative regulation of macroautophagy / protein kinase A binding / regulation of epidermal cell division / protein kinase C inhibitor activity / neuromuscular junction development / regulation of cAMP/PKA signal transduction / positive regulation of epidermal cell differentiation / keratinocyte development / regulation of mitochondrial fission / keratinization / regulation of locomotion / regulation of synaptic vesicle exocytosis / microvillus / Golgi organization / exploration behavior / intracellular distribution of mitochondria / regulation of cell-cell adhesion / endoplasmic reticulum exit site / autolysosome / locomotory exploration behavior / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / negative regulation of Notch signaling pathway / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / MAP kinase kinase kinase activity / regulation of synaptic vesicle endocytosis / negative regulation of keratinocyte proliferation / canonical Wnt signaling pathway / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of synaptic transmission, glutamatergic / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / presynaptic cytosol / Rho protein signal transduction / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / neuron projection morphogenesis / positive regulation of protein localization / phagocytic vesicle
Similarity search - Function
: / : / : / LRRK2 ARM repeat / LRRK2 ANK repeat / LRRK2 beta propeller / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain ...: / : / : / LRRK2 ARM repeat / LRRK2 ANK repeat / LRRK2 beta propeller / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Leucine-rich repeats, bacterial type / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.327 Å
AuthorsStevers, L.M. / de Vries, R.M.J.M. / Ottmann, C.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural interface between LRRK2 and 14-3-3 protein.
Authors: Stevers, L.M. / de Vries, R.M. / Doveston, R.G. / Milroy, L.G. / Brunsveld, L. / Ottmann, C.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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 / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Leucine-rich repeat serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2646
Polymers28,1092
Non-polymers1564
Water6,900383
1
A: 14-3-3 protein sigma
P: Leucine-rich repeat serine/threonine-protein kinase 2
hetero molecules

A: 14-3-3 protein sigma
P: Leucine-rich repeat serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,52812
Polymers56,2174
Non-polymers3118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.291, 112.030, 62.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

CA

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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 Leucine-rich repeat serine/threonine-protein kinase 2 / Dardarin


Mass: 1565.624 Da / Num. of mol.: 1 / Fragment: UNP Residues 929-941 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q5S007, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#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.: 383 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: HEPES, NaCl, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.088→50 Å / Num. all: 66705 / Num. obs: 380505 / % possible obs: 99.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Net I/σ(I): 21.96
Reflection shellResolution: 1.33→1.4 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 110595 / CC1/2: 0.86 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.11 2567phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BTV

5btv


Resolution: 1.327→45.458 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 22.38
RfactorNum. reflection% reflection
Rfree0.2005 6426 5 %
Rwork0.1865 --
obs0.1872 128449 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.327→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 4 383 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072042
X-RAY DIFFRACTIONf_angle_d0.822772
X-RAY DIFFRACTIONf_dihedral_angle_d17.341818
X-RAY DIFFRACTIONf_chiral_restr0.064302
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3268-1.34190.36921850.38653559X-RAY DIFFRACTION87
1.3419-1.35770.33172170.32594120X-RAY DIFFRACTION100
1.3577-1.37420.32392180.32284079X-RAY DIFFRACTION100
1.3742-1.39160.34212160.30224036X-RAY DIFFRACTION100
1.3916-1.40990.3212100.29894071X-RAY DIFFRACTION100
1.4099-1.42930.30292170.28844059X-RAY DIFFRACTION100
1.4293-1.44970.28812190.28744144X-RAY DIFFRACTION100
1.4497-1.47130.2992160.28424080X-RAY DIFFRACTION100
1.4713-1.49430.30092180.28274061X-RAY DIFFRACTION100
1.4943-1.51880.23872160.27994069X-RAY DIFFRACTION100
1.5188-1.5450.27922150.27994110X-RAY DIFFRACTION100
1.545-1.57310.29812200.26014083X-RAY DIFFRACTION100
1.5731-1.60340.27082160.24734094X-RAY DIFFRACTION100
1.6034-1.63610.29042170.23744042X-RAY DIFFRACTION100
1.6361-1.67170.21982190.20784075X-RAY DIFFRACTION100
1.6717-1.71060.26082080.19894093X-RAY DIFFRACTION100
1.7106-1.75330.20412170.18484109X-RAY DIFFRACTION100
1.7533-1.80070.18852110.18994062X-RAY DIFFRACTION100
1.8007-1.85370.19482160.17064079X-RAY DIFFRACTION100
1.8537-1.91360.19142170.16794117X-RAY DIFFRACTION100
1.9136-1.9820.17672140.15864077X-RAY DIFFRACTION100
1.982-2.06130.15452150.15774062X-RAY DIFFRACTION100
2.0613-2.15510.16622130.15824113X-RAY DIFFRACTION100
2.1551-2.26870.17272140.15554098X-RAY DIFFRACTION100
2.2687-2.41090.1522130.15384072X-RAY DIFFRACTION100
2.4109-2.5970.17632140.16774122X-RAY DIFFRACTION100
2.597-2.85830.20572110.17394050X-RAY DIFFRACTION100
2.8583-3.27180.17192190.16544080X-RAY DIFFRACTION100
3.2718-4.12170.1692140.14884113X-RAY DIFFRACTION100
4.1217-45.48490.18232110.17614094X-RAY DIFFRACTION100

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