[English] 日本語
Yorodumi
- PDB-6byr: Structures of the PKA RI alpha holoenzyme with the FLHCC driver J... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 subunitCAMP-dependent pathway
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 connecting piece / sperm head / ROBO receptors bind AKAP5 / negative regulation of inclusion body assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm connecting piece / sperm head / ROBO receptors bind AKAP5 / negative regulation of inclusion body assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / HDL assembly / high-density lipoprotein particle assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / PKA activation / regulation of protein binding / Hedgehog 'off' state / Rap1 signalling / nucleotide-activated protein kinase complex / positive regulation of ATP-dependent activity / renal water homeostasis / regulation of protein processing / transcription regulator inhibitor activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cell communication by electrical coupling involved in cardiac conduction / sarcomere organization / cAMP-dependent protein kinase / cellular response to cold / cardiac muscle cell proliferation / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / ATPase activator activity / axoneme / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / chaperone cofactor-dependent protein refolding / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / immunological synapse / mesoderm formation / regulation of cardiac conduction / HSF1-dependent transactivation / RET signaling / DARPP-32 events / response to unfolded protein / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of HSF1-mediated heat shock response / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction / Attenuation phase / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / regulation of cellular response to heat / protein folding chaperone / protein kinase A signaling / forebrain development / cAMP binding / positive regulation of gluconeogenesis / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / Hsp70 protein binding / Recruitment of NuMA to mitotic centrosomes / cellular response to epinephrine stimulus / calcium channel complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of heart rate / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / CD209 (DC-SIGN) signaling / multivesicular body / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis
Similarity search - Function
DnaJ domain / cAMP-dependent protein kinase regulatory subunit / 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 / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site ...DnaJ domain / cAMP-dependent protein kinase regulatory subunit / 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 / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / 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 / Jelly Rolls / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 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 (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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / CAMP-dependent pathway


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more