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

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Basic information

Entry
Database: PDB / ID: 5myc
TitleCrystal structure of human 14-3-3 sigma in complex with LRRK2 peptide pS910
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 / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of cell projection organization / tangential migration from the subventricular zone to the olfactory bulb / protein localization to endoplasmic reticulum exit site / GTP-dependent protein kinase activity ...caveola neck / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of cell projection organization / tangential migration from the subventricular zone to the olfactory bulb / protein localization to endoplasmic reticulum exit site / GTP-dependent protein kinase activity / regulation of SNARE complex assembly / regulation of neuroblast proliferation / regulation of ER to Golgi vesicle-mediated transport / 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 / regulation of synaptic vesicle transport / regulation of CAMKK-AMPK signaling cascade / regulation of lysosomal lumen pH / amphisome / co-receptor binding / mitochondrion localization / regulation of dopamine receptor signaling pathway / regulation of retrograde transport, endosome to Golgi / regulation of neuron maturation / positive regulation of microglial cell activation / positive regulation of synaptic vesicle endocytosis / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / negative regulation of excitatory postsynaptic potential / regulation of cAMP/PKA signal transduction / JUN kinase kinase kinase activity / olfactory bulb development / neuron projection arborization / striatum development / multivesicular body, internal vesicle / regulation of dendritic spine morphogenesis / protein localization to mitochondrion / cellular response to dopamine / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum organization / positive regulation of protein autoubiquitination / Wnt signalosome / positive regulation of programmed cell death / negative regulation of protein processing / GTP metabolic process / syntaxin-1 binding / negative regulation of GTPase activity / regulation of canonical Wnt signaling pathway / regulation of reactive oxygen species metabolic process / lysosome organization / Golgi-associated vesicle / clathrin binding / regulation of locomotion / negative regulation of macroautophagy / PTK6 promotes HIF1A stabilization / protein kinase A binding / neuromuscular junction development / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / regulation of mitochondrial fission / keratinocyte development / keratinization / Golgi organization / regulation of synaptic vesicle exocytosis / exploration behavior / microvillus / intracellular distribution of mitochondria / regulation of cell-cell adhesion / autolysosome / locomotory exploration behavior / endoplasmic reticulum exit site / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of Notch signaling pathway / regulation of synaptic vesicle endocytosis / cellular response to manganese ion / MAP kinase kinase kinase activity / Activation of BAD and translocation to mitochondria / Rho protein signal transduction / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / presynaptic cytosol / regulation of synaptic transmission, glutamatergic / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of protein kinase activity / phagocytic vesicle / positive regulation of protein localization
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 / Leucine-rich repeats, bacterial type / 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 / 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. / WD40-repeat-containing domain superfamily / Protein kinase domain / 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: 1.459 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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 2.1Nov 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)31,1406
Polymers31,0022
Non-polymers1394
Water7,440413
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)62,28112
Polymers62,0034
Non-polymers2778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area6510 Å2
ΔGint-86 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.517, 112.411, 62.689
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-301-

CA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#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: 4458.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q5S007, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 417 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: HEPES, NaCl2, PEG400, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97862 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: 0.97862 Å / Relative weight: 1
ReflectionResolution: 1.088→45.618 Å / Num. obs: 116840 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.035 / Rrim(I) all: 0.129 / Net I/σ(I): 14.99
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 85995 / CC1/2: 0.75 / % possible all: 98.7

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Processing

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

5btv


Resolution: 1.459→41.848 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1887 4897 5.01 %
Rwork0.166 --
obs0.1671 97760 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.459→41.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 4 413 2371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062120
X-RAY DIFFRACTIONf_angle_d0.752882
X-RAY DIFFRACTIONf_dihedral_angle_d19.178853
X-RAY DIFFRACTIONf_chiral_restr0.06314
X-RAY DIFFRACTIONf_plane_restr0.004377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4593-1.47590.33831500.30142889X-RAY DIFFRACTION93
1.4759-1.49320.33821650.26823100X-RAY DIFFRACTION100
1.4932-1.51150.27541670.26153122X-RAY DIFFRACTION100
1.5115-1.53060.28771610.25293083X-RAY DIFFRACTION100
1.5306-1.55070.24781670.24823095X-RAY DIFFRACTION100
1.5507-1.5720.27721610.24113074X-RAY DIFFRACTION100
1.572-1.59440.25571630.24493133X-RAY DIFFRACTION100
1.5944-1.61820.25291660.2333149X-RAY DIFFRACTION100
1.6182-1.64350.26961630.21793051X-RAY DIFFRACTION100
1.6435-1.67050.20451630.20413137X-RAY DIFFRACTION100
1.6705-1.69930.21811640.18723131X-RAY DIFFRACTION100
1.6993-1.73020.19891610.1933054X-RAY DIFFRACTION100
1.7302-1.76350.16971630.193081X-RAY DIFFRACTION100
1.7635-1.79940.20561650.1853127X-RAY DIFFRACTION100
1.7994-1.83860.20131670.17533116X-RAY DIFFRACTION100
1.8386-1.88130.17211580.17383086X-RAY DIFFRACTION100
1.8813-1.92840.17481590.17033073X-RAY DIFFRACTION100
1.9284-1.98050.21921670.17193127X-RAY DIFFRACTION100
1.9805-2.03880.19331620.16483095X-RAY DIFFRACTION100
2.0388-2.10460.18541660.15363104X-RAY DIFFRACTION100
2.1046-2.17980.19751650.15013148X-RAY DIFFRACTION100
2.1798-2.26710.1721630.14433043X-RAY DIFFRACTION100
2.2671-2.37030.18011660.14883092X-RAY DIFFRACTION100
2.3703-2.49520.17141640.15013147X-RAY DIFFRACTION100
2.4952-2.65150.16591660.1463074X-RAY DIFFRACTION100
2.6515-2.85620.15651640.15993116X-RAY DIFFRACTION100
2.8562-3.14360.18891630.14983101X-RAY DIFFRACTION100
3.1436-3.59820.15391640.13773097X-RAY DIFFRACTION100
3.5982-4.53250.16311610.13243105X-RAY DIFFRACTION100
4.5325-41.86560.17931630.16823113X-RAY DIFFRACTION100

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