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- PDB-4dnl: Crystal structure of a C2 domain of a protein kinase C alpha (PRK... -

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Basic information

Entry
Database: PDB / ID: 4dnl
TitleCrystal structure of a C2 domain of a protein kinase C alpha (PRKCA) from Homo sapiens at 1.90 A resolution
ComponentsProtein kinase C alpha type
KeywordsTRANSFERASE / calcium-dependent phospholipid binding / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / positive regulation of angiotensin-activated signaling pathway / desmosome assembly / positive regulation of dense core granule biogenesis / histone H3T6 kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Trafficking of GluR2-containing AMPA receptors ...Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / positive regulation of angiotensin-activated signaling pathway / desmosome assembly / positive regulation of dense core granule biogenesis / histone H3T6 kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Trafficking of GluR2-containing AMPA receptors / ROBO receptors bind AKAP5 / WNT5A-dependent internalization of FZD4 / Acetylcholine regulates insulin secretion / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / mitotic nuclear membrane disassembly / regulation of platelet aggregation / positive regulation of macrophage differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / alphav-beta3 integrin-PKCalpha complex / Calmodulin induced events / Syndecan interactions / Regulation of KIT signaling / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / RET signaling / positive regulation of cell adhesion / RHO GTPases Activate NADPH Oxidases / positive regulation of blood vessel endothelial cell migration / positive regulation of bone resorption / positive regulation of endothelial cell proliferation / regulation of mRNA stability / EGFR Transactivation by Gastrin / positive regulation of endothelial cell migration / SHC1 events in ERBB2 signaling / positive regulation of mitotic cell cycle / response to interleukin-1 / post-translational protein modification / ciliary basal body / VEGFR2 mediated cell proliferation / mitochondrial membrane / apoptotic signaling pathway / peptidyl-threonine phosphorylation / Signaling by SCF-KIT / G alpha (z) signalling events / positive regulation of angiogenesis / Inactivation, recovery and regulation of the phototransduction cascade / integrin binding / Ca2+ pathway / peptidyl-serine phosphorylation / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Classical Protein Kinase C alpha, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) ...Classical Protein Kinase C alpha, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / C2 domain / C2 domain profile. / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein kinase C alpha type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a C2 domain of a protein kinase C alpha (PRKCA) from Homo sapiens at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references / Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

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Assembly

Deposited unit
A: Protein kinase C alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4782
Polymers16,4551
Non-polymers231
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.035, 58.035, 88.714
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Protein kinase C alpha type / PKC-A / PKC-alpha


Mass: 16455.057 Da / Num. of mol.: 1 / Fragment: C2 domain residues 155-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NM_002737, PKCA, PRKACA, PRKCA / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: P17252, protein kinase C
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 155-293 OF THE TARGET SEQUENCE.

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30.00% polyethylene glycol 6000, 0.1M sodium citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9464,0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94641
20.97951
ReflectionResolution: 1.9→29.571 Å / Num. obs: 14172 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.326 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.970.8861.59587258495.9
1.97-2.050.552.410236269499.7
2.05-2.140.3733.59616253299.9
2.14-2.250.2585.399602622100
2.25-2.390.197.29998262399.9
2.39-2.580.12210.610461274299.9
2.58-2.840.07915.199172608100
2.84-3.250.04723.19987265299.8
3.25-4.080.031359641262299.7
4.080.02540.69760267399.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.571 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.689 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.133
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. SODIUM ION (NA) IS MODELED BASED ON ITS PRESENCE IN THE CRYSTALLLIZATION CONDITION AND GEOMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 709 5 %RANDOM
Rwork0.1862 ---
obs0.1883 14132 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 119.49 Å2 / Biso mean: 57.0174 Å2 / Biso min: 34.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 1 55 1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021168
X-RAY DIFFRACTIONr_bond_other_d0.0020.02831
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9781589
X-RAY DIFFRACTIONr_angle_other_deg0.89832035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06824.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61415217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.378158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 44 -
Rwork0.245 875 -
all-919 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 31.486 Å / Origin y: 14.038 Å / Origin z: 9.1 Å
111213212223313233
T0.1099 Å20.0204 Å2-0.023 Å2-0.0484 Å2-0.0538 Å2--0.1401 Å2
L3.4894 °2-0.4296 °21.3272 °2-2.7306 °2-1.3256 °2--4.2902 °2
S0.2181 Å °0.2053 Å °-0.5924 Å °-0.0028 Å °-0.0169 Å °0.0813 Å °0.17 Å °0.1314 Å °-0.2012 Å °

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