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- PDB-6em7: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 6em7
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp120 and ADP
Components
  • UPF0418 protein FAM164A
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Complex / peptidic ligand
Function / homology
Function and homology information


cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / regulation of osteoblast differentiation ...cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / regulation of cell cycle / postsynapse / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / beta-D-ribopyranose / UPF0418 protein FAM164A / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.238 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe Corporation Germany
CitationJournal: Acs Omega / Year: 2019
Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G.
History
DepositionOct 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
D: UPF0418 protein FAM164A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8746
Polymers43,0602
Non-polymers8144
Water6,035335
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-20 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.481, 80.009, 84.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AD

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide UPF0418 protein FAM164A


Mass: 1946.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI 5-22 with N20RBS / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48
#5: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 338 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 55 mM lithium chloride, 10 mM magnesium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM ADP, 20% v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.24→42.151 Å / Num. obs: 122237 / % possible obs: 98.4 % / Redundancy: 4.42 % / CC1/2: 0.999 / Rsym value: 0.04 / Net I/σ(I): 19.02
Reflection shellResolution: 1.24→1.31 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.83 / Num. unique obs: 19106 / CC1/2: 0.828 / Rsym value: 0.487 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.238→42.151 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1565 6112 5 %Random selection
Rwork0.1385 ---
obs0.1394 122229 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.238→42.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 47 335 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093099
X-RAY DIFFRACTIONf_angle_d1.1544226
X-RAY DIFFRACTIONf_dihedral_angle_d21.0921129
X-RAY DIFFRACTIONf_chiral_restr0.083454
X-RAY DIFFRACTIONf_plane_restr0.008542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2384-1.25250.30331830.28543490X-RAY DIFFRACTION90
1.2525-1.26720.2722020.24223829X-RAY DIFFRACTION98
1.2672-1.28270.24761990.21323770X-RAY DIFFRACTION98
1.2827-1.29890.24092000.19243807X-RAY DIFFRACTION98
1.2989-1.3160.20442010.17993818X-RAY DIFFRACTION97
1.316-1.33410.20311990.1643774X-RAY DIFFRACTION98
1.3341-1.35310.20312010.14763835X-RAY DIFFRACTION98
1.3531-1.37330.16382010.13513811X-RAY DIFFRACTION98
1.3733-1.39480.16012010.12543822X-RAY DIFFRACTION98
1.3948-1.41760.15222020.11813846X-RAY DIFFRACTION98
1.4176-1.44210.14072020.11553833X-RAY DIFFRACTION98
1.4421-1.46830.14392040.11313868X-RAY DIFFRACTION99
1.4683-1.49660.13962030.10983867X-RAY DIFFRACTION99
1.4966-1.52710.13982020.10883838X-RAY DIFFRACTION99
1.5271-1.56030.13962030.11093855X-RAY DIFFRACTION98
1.5603-1.59660.1392030.10833862X-RAY DIFFRACTION99
1.5966-1.63650.12932040.10383867X-RAY DIFFRACTION99
1.6365-1.68080.1332050.09933886X-RAY DIFFRACTION99
1.6808-1.73030.11722040.13888X-RAY DIFFRACTION99
1.7303-1.78610.13352050.10233893X-RAY DIFFRACTION99
1.7861-1.84990.13242060.11243914X-RAY DIFFRACTION99
1.8499-1.9240.13882050.11893898X-RAY DIFFRACTION99
1.924-2.01160.14892070.12293926X-RAY DIFFRACTION99
2.0116-2.11760.15242070.12853928X-RAY DIFFRACTION99
2.1176-2.25030.1412060.12563931X-RAY DIFFRACTION99
2.2503-2.4240.14872080.12833949X-RAY DIFFRACTION99
2.424-2.66790.15742090.14283964X-RAY DIFFRACTION99
2.6679-3.05390.17142100.15853989X-RAY DIFFRACTION100
3.0539-3.84720.16532110.16084019X-RAY DIFFRACTION99
3.8472-42.17490.15752190.15874140X-RAY DIFFRACTION98

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