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- PDB-3pfq: Crystal Structure and Allosteric Activation of Protein Kinase C b... -

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Basic information

Entry
Database: PDB / ID: 3pfq
TitleCrystal Structure and Allosteric Activation of Protein Kinase C beta II
ComponentsProtein kinase C beta type
KeywordsTRANSFERASE / Kinase / Phosphorylation
Function / homology
Function and homology information


dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / cellular response to carbohydrate stimulus / protein kinase C signaling / Activation of NF-kappaB in B cells / VEGFR2 mediated cell proliferation / positive regulation of odontogenesis of dentin-containing tooth / spectrin ...dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / cellular response to carbohydrate stimulus / protein kinase C signaling / Activation of NF-kappaB in B cells / VEGFR2 mediated cell proliferation / positive regulation of odontogenesis of dentin-containing tooth / spectrin / regulation of D-glucose transmembrane transport / WNT5A-dependent internalization of FZD4 / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / RHO GTPases Activate NADPH Oxidases / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / negative regulation of D-glucose transmembrane transport / diacylglycerol-dependent serine/threonine kinase activity / response to vitamin D / response to angiotensin / regulation of growth / positive regulation of vascular endothelial growth factor receptor signaling pathway / nuclear androgen receptor binding / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / Trafficking of GluR2-containing AMPA receptors / B cell activation / presynaptic cytosol / response to glucose / calcium channel regulator activity / presynaptic modulation of chemical synaptic transmission / calyx of Held / negative regulation of insulin receptor signaling pathway / post-translational protein modification / protein kinase C binding / B cell receptor signaling pathway / brush border membrane / positive regulation of insulin secretion / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / adaptive immune response / histone binding / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / histone H3T6 kinase activity / intracellular signal transduction / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein kinase C beta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsLeonard, T.A. / Rozycki, B. / Saidi, L.F. / Hummer, G. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Crystal Structure and Allosteric Activation of Protein Kinase C beta II
Authors: Leonard, T.A. / Rozycki, B. / Saidi, L.F. / Hummer, G. / Hurley, J.H.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 11, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / diffrn_source ...diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 1.4Sep 6, 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_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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0117
Polymers77,2541
Non-polymers7576
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.270, 114.270, 170.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein kinase C beta type / PKC-beta


Mass: 77253.859 Da / Num. of mol.: 1 / Fragment: PKC beta II / Mutation: C70S C217S C622S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkcb, Pkcb, Prkcb1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P68403, protein kinase C
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has protein modificationY
Sequence detailsTHE VARIANT SEQUENCE CORRESPONDS TO UNP P68403-2, ISOFORM BETA-II.

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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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris, pH 8.5, 3% PEG8K, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2009 / Details: mirrors
RadiationMonochromator: K-B pair of biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 4→57.1 Å / Num. all: 10670 / Num. obs: 10670 / % possible obs: 93.9 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8
Reflection shellResolution: 4→4.22 Å / % possible all: 88

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2I0E and 1A25

2i0e

1a25


Resolution: 4→57.1 Å / σ(F): 1.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2445 508 RANDOM
Rwork0.1931 --
obs0.2445 10670 -
all-10670 -
Refinement stepCycle: LAST / Resolution: 4→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4237 0 36 0 4273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg0.878
LS refinement shellResolution: 4→4.14 Å
RfactorNum. reflection% reflection
Rfree0.2909 48 -
Rwork0.2673 --
obs-919 86.3 %

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