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- PDB-3ugl: Structural and functional characterization of an anesthetic bindi... -

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Basic information

Entry
Database: PDB / ID: 3ugl
TitleStructural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta
ComponentsProteine kinase C delta type
KeywordsMETAL BINDING PROTEIN / Proteine kinase C delta / PHOSPHOTRANSFERASE / Anesthetic binding site
Function / homology
Function and homology information


DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / Effects of PIP2 hydrolysis / HuR (ELAVL1) binds and stabilizes mRNA ...DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / Effects of PIP2 hydrolysis / HuR (ELAVL1) binds and stabilizes mRNA / Interferon gamma signaling / Calmodulin induced events / TIR domain binding / endolysosome / positive regulation of ceramide biosynthetic process / negative regulation of peptidyl-tyrosine phosphorylation / Role of phospholipids in phagocytosis / termination of signal transduction / negative regulation of filopodium assembly / protein kinase C / cellular response to hydroperoxide / negative regulation of glial cell apoptotic process / collagen metabolic process / CLEC7A (Dectin-1) signaling / D-aspartate import across plasma membrane / diacylglycerol-dependent serine/threonine kinase activity / RHO GTPases Activate NADPH Oxidases / negative regulation of actin filament polymerization / neutrophil activation / regulation of phosphorylation / negative regulation of platelet aggregation / cellular response to angiotensin / postsynaptic cytosol / B cell proliferation / immunoglobulin mediated immune response / enzyme activator activity / insulin receptor substrate binding / positive regulation of apoptotic signaling pathway / positive regulation of protein dephosphorylation / negative regulation of insulin receptor signaling pathway / Neutrophil degranulation / post-translational protein modification / cell chemotaxis / positive regulation of superoxide anion generation / regulation of actin cytoskeleton organization / positive regulation of glucose import / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cellular response to hydrogen peroxide / nuclear matrix / positive regulation of protein import into nucleus / cellular response to UV / cell-cell junction / cellular senescence / cellular response to oxidative stress / peptidyl-serine phosphorylation / response to oxidative stress / positive regulation of MAPK cascade / protein kinase activity / intracellular signal transduction / defense response to bacterium / cell cycle / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / mitochondrion / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. ...Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / C2 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
cyclopropylmethanol / PHOSPHATE ION / Protein kinase C delta type
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.357 Å
AuthorsShanmugasundararaj, S. / Stehle, T. / Miller, K.W.
Citation
Journal: Biophys.J. / Year: 2012
Title: Structural and Functional Characterization of an Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta
Authors: Shanmugasundararaj, S. / Das, J. / Sandberg, W.S. / Zhou, X. / Wang, D. / Messing, R.O. / Bruzik, K.S. / Stehle, T. / Miller, K.W.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of the cys2 activator binding domain of protein kinase C delta in complex with phorbol ester
Authors: Zhang, G. / Kazanietz, M.G. / Blumberg, P.M. / Hurley, J.H.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteine kinase C delta type
B: Proteine kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,44411
Polymers14,7532
Non-polymers6919
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.876, 32.522, 49.816
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proteine kinase C delta type / nPKC-delta


Mass: 7376.554 Da / Num. of mol.: 2 / Fragment: C1B Subdomain of PKC delta, UNP residues 231-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcd, Pkcd / Production host: Escherichia coli (E. coli) / References: UniProt: P28867, protein kinase C
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-09V / cyclopropylmethanol


Mass: 72.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350 in 0.2 M ammonium sulfate and 25 mM HEPES pH 7.2. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2004
RadiationMonochromator: SI(111) CHANNEL CULT MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→10 Å / Num. all: 30362 / Num. obs: 28279 / % possible obs: 92.51 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PTQ

1ptq


Resolution: 1.357→9.986 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.17 1936 6.85 %10%
Rwork0.1468 ---
all0.1484 30362 --
obs0.1484 28279 92.51 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.422 Å2 / ksol: 0.546 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3611 Å2-0 Å24.1708 Å2
2---3.7351 Å2-0 Å2
3---1.374 Å2
Refinement stepCycle: LAST / Resolution: 1.357→9.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 29 211 1264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061080
X-RAY DIFFRACTIONf_angle_d1.0921453
X-RAY DIFFRACTIONf_dihedral_angle_d13.351391
X-RAY DIFFRACTIONf_chiral_restr0.08151
X-RAY DIFFRACTIONf_plane_restr0.004183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.357-1.39040.1929720.21131148X-RAY DIFFRACTION57
1.3904-1.42790.2221150.18941543X-RAY DIFFRACTION76
1.4279-1.46980.22211350.16151807X-RAY DIFFRACTION90
1.4698-1.51710.18671410.13941879X-RAY DIFFRACTION93
1.5171-1.57110.16141350.13031900X-RAY DIFFRACTION95
1.5711-1.63370.15871460.11961971X-RAY DIFFRACTION96
1.6337-1.70770.15131410.11451980X-RAY DIFFRACTION98
1.7077-1.79730.14951560.11281946X-RAY DIFFRACTION98
1.7973-1.90910.16331400.12912038X-RAY DIFFRACTION99
1.9091-2.05540.16141510.13411990X-RAY DIFFRACTION99
2.0554-2.260.17631500.13982010X-RAY DIFFRACTION99
2.26-2.58210.181470.14632051X-RAY DIFFRACTION100
2.5821-3.23470.18111540.16612054X-RAY DIFFRACTION100
3.2347-9.98610.15661530.16362026X-RAY DIFFRACTION96

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