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- PDB-6e21: Joint X-ray/neutron structure of PKAc with products Sr2-ADP and p... -

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Basic information

Entry
Database: PDB / ID: 6.0E+21
TitleJoint X-ray/neutron structure of PKAc with products Sr2-ADP and phosphorylated peptide SP20
Components
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
  • pSP20
KeywordsTRANSFERASE / protein kinase / phosphorylated product complex
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / Mitochondrial protein degradation / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / Mitochondrial protein degradation / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / negative regulation of cAMP-dependent protein kinase activity / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / protein kinase A catalytic subunit binding / plasma membrane raft / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / 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. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DEUTERATED WATER / STRONTIUM ION / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKovalevsky, A. / Gerlits, O.O. / Taylor, S.
Citation
Journal: Sci Adv / Year: 2019
Title: Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex.
Authors: Gerlits, O. / Weiss, K.L. / Blakeley, M.P. / Veglia, G. / Taylor, S.S. / Kovalevsky, A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 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 / diffrn_radiation_wavelength / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _refine_hist.d_res_low / _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

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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
B: pSP20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4485
Polymers43,8462
Non-polymers6023
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22570 Å2
ΔGint-63 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.332, 79.898, 100.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41566.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein/peptide pSP20


Mass: 2279.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925*PLUS
#3: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES, pH 6.5, 5 mM DTT, PEG4000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORILL LADI III22.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATESep 15, 2015osmic varimax
LADI III2IMAGE PLATESep 18, 2015collimators
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
341
Reflection

Entry-ID: 6.0E+21

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-403017591.74.20.069114.3
2.5-4010426623.40.15327.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I) obs% possible all
2-2.074.20.54211.991
2.5-2.641.90.18125.243.6

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Processing

Software
NameVersionClassification
nCNS1.0.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
LAUEGENdata reduction
LSCALEdata scaling
CNSphasing
Refinement

Biso max: 79.8 Å2 / Biso mean: 30.03 Å2 / Biso min: 8.86 Å2 / % reflection Rfree: 5 % / R Free selection details: random / Cross valid method: FREE R-VALUE / σ(F): 3 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: joint X-ray/neutron ML / Bsol: 42.5881 Å2 / ksol: 0.307086 e/Å3

Starting modelResolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection obs% reflection obs (%)
PDB entry 4IAY

4iay

2-40X-RAY DIFFRACTION0.2170.18711702411973.3
2.5-40NEUTRON DIFFRACTION0.2750.2264741001260
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.240.23
Luzzati d res low-5
Luzzati sigma a0.140.16
Luzzati d res high-2
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.40.36
Luzzati d res low-5
Luzzati sigma a0.590.61
Luzzati d res high-2.5
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 29 152 3121
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg29.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.71
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg29.5
NEUTRON DIFFRACTIONx_torsion_impr_deg0.71
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.2058550.2121723X-RAY DIFFRACTION0.0224039180844.8
2.09-2.20.2191195.10.2192232X-RAY DIFFRACTION0.024086235157.5
2.2-2.340.23713450.2232551X-RAY DIFFRACTION0.024028268566.7
2.34-2.520.2461645.40.2282899X-RAY DIFFRACTION0.0194101306374.7
2.52-2.770.2321725.20.2263124X-RAY DIFFRACTION0.0184095329680.5
2.77-3.170.2311754.90.2193409X-RAY DIFFRACTION0.0174105358487.3
3.17-40.1931794.60.193684X-RAY DIFFRACTION0.0144170386392.6
4-38.30.19920850.1863923X-RAY DIFFRACTION0.0144316413195.7
2.5-2.610.353450.354819NEUTRON DIFFRACTION0.06208685340.9
2.61-2.750.371485.30.38850NEUTRON DIFFRACTION0.054209789842.8
2.75-2.920.412394.10.342917NEUTRON DIFFRACTION0.066211495645.2
2.92-3.150.3615250.313990NEUTRON DIFFRACTION0.052105104249.5
3.15-3.470.259584.60.2251199NEUTRON DIFFRACTION0.0342128125759.1
3.47-3.970.135593.80.1721477NEUTRON DIFFRACTION0.0182133153672
3.97-50.144925.10.1491724NEUTRON DIFFRACTION0.0152165181683.9
5-38.30.291985.10.2651808NEUTRON DIFFRACTION0.0292262190684.3

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