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- PDB-6byr: Structures of the PKA RI alpha holoenzyme with the FLHCC driver J... -

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Entry
Database: PDB / ID: 6byr
TitleStructures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha
Components
  • DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera
  • cAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsSIGNALING PROTEIN / Protein complex / PKA holoenzyme / Fibrolamellar Hepatocellular Carcinoma
Function / homology
Function and homology information


: / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm head-tail coupling apparatus / ROBO receptors bind AKAP5 / sperm head / HDL assembly / negative regulation of inclusion body assembly / PKA activation in glucagon signalling / DARPP-32 events ...: / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm head-tail coupling apparatus / ROBO receptors bind AKAP5 / sperm head / HDL assembly / negative regulation of inclusion body assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / channel activator activity / Factors involved in megakaryocyte development and platelet production / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / PKA activation / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / Hedgehog 'off' state / high-density lipoprotein particle assembly / Rap1 signalling / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / sarcomere organization / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of interleukin-2 production / PKA activation / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / Triglyceride catabolism / ciliary base / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / forebrain development / intracellular potassium ion homeostasis / ATPase activator activity / : / mesoderm formation / RET signaling / cAMP/PKA signal transduction / Interleukin-3, Interleukin-5 and GM-CSF signaling / immunological synapse / plasma membrane raft / axoneme / PKA activation in glucagon signalling / Regulation of MECP2 expression and activity / DARPP-32 events / Regulation of HSF1-mediated heat shock response / regulation of cardiac conduction / HSF1-dependent transactivation / regulation of macroautophagy / cardiac muscle cell proliferation / response to unfolded protein / regulation of cardiac muscle contraction / sperm flagellum / Attenuation phase / postsynaptic modulation of chemical synaptic transmission / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / cAMP binding / Hedgehog 'off' state / transcription regulator inhibitor activity / regulation of cellular response to heat / Ion homeostasis / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / sperm midpiece / multivesicular body / Hsp70 protein binding / cellular response to epinephrine stimulus / calcium channel complex / positive regulation of gluconeogenesis / protein folding chaperone / protein serine/threonine/tyrosine kinase activity / Mitochondrial protein degradation / cellular response to glucagon stimulus / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / acrosomal vesicle / CD209 (DC-SIGN) signaling / positive regulation of calcium-mediated signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of heart rate
Similarity search - Function
: / DnaJ domain / cAMP-dependent protein kinase regulatory subunit / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : ...: / DnaJ domain / cAMP-dependent protein kinase regulatory subunit / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Cyclic nucleotide-binding domain signature 2. / Chaperone J-domain superfamily / DnaJ domain / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Helix Hairpins / 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. / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit / cAMP-dependent protein kinase catalytic subunit alpha / DnaJ homolog subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.661 Å
AuthorsCao, B. / Lu, T.W. / Martinez Fiesco, J.A. / Tomasini, M. / Fan, L. / Simon, S.M. / Taylor, S.S. / Zhang, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2019
Title: Structures of the PKA RI alpha Holoenzyme with the FLHCC Driver J-PKAc alpha or Wild-Type PKAc alpha.
Authors: Cao, B. / Lu, T.W. / Martinez Fiesco, J.A. / Tomasini, M. / Fan, L. / Simon, S.M. / Taylor, S.S. / Zhang, P.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
C: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,92810
Polymers180,8174
Non-polymers1,1126
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9645
Polymers90,4082
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-35 kcal/mol
Surface area33090 Å2
MethodPISA
3
C: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9645
Polymers90,4082
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-37 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.504, 166.504, 332.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera / DnaJ protein homolog 1 / Heat shock 40 kDa protein 1 / Heat shock protein 40 / Human DnaJ protein 1 ...DnaJ protein homolog 1 / Heat shock 40 kDa protein 1 / Heat shock protein 40 / Human DnaJ protein 1 / hDj-1 / PKA C-alpha


Mass: 47591.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB1, DNAJ1, HDJ1, HSPF1, PRKACA, PKACA / Production host: Escherichia coli (E. coli)
References: UniProt: P25685, UniProt: P17612, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit


Mass: 42816.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKAR1A / Production host: Escherichia coli (E. coli) / References: UniProt: P00514
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.66→50 Å / Num. obs: 30877 / % possible obs: 100 % / Redundancy: 21.3 % / Rsym value: 0.135 / Net I/σ(I): 29.5
Reflection shellResolution: 3.66→3.79 Å / Redundancy: 22.2 % / Mean I/σ(I) obs: 8.7 / Num. unique obs: 3018 / Rsym value: 0.498 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCS and 4WB7

2qcs

4wb7


Resolution: 3.661→48.914 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.84
RfactorNum. reflection% reflection
Rfree0.2495 2000 6.49 %
Rwork0.1995 --
obs0.2028 30794 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.661→48.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11292 0 66 0 11358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311608
X-RAY DIFFRACTIONf_angle_d0.62315670
X-RAY DIFFRACTIONf_dihedral_angle_d22.0934400
X-RAY DIFFRACTIONf_chiral_restr0.0441646
X-RAY DIFFRACTIONf_plane_restr0.0042024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6611-3.75260.31621390.2552000X-RAY DIFFRACTION100
3.7526-3.8540.30771400.22172013X-RAY DIFFRACTION100
3.854-3.96740.24811400.21432032X-RAY DIFFRACTION100
3.9674-4.09540.26811380.21691982X-RAY DIFFRACTION100
4.0954-4.24170.26551420.22122040X-RAY DIFFRACTION100
4.2417-4.41140.26231400.20692012X-RAY DIFFRACTION100
4.4114-4.6120.26281400.19832019X-RAY DIFFRACTION100
4.612-4.8550.25721420.19512038X-RAY DIFFRACTION100
4.855-5.15880.25771420.19282058X-RAY DIFFRACTION100
5.1588-5.55670.22441440.20232064X-RAY DIFFRACTION100
5.5567-6.11490.27841430.21732058X-RAY DIFFRACTION100
6.1149-6.99750.27921450.22142090X-RAY DIFFRACTION100
6.9975-8.80770.19381470.18942126X-RAY DIFFRACTION100
8.8077-48.9180.21871580.16192262X-RAY DIFFRACTION100

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