[English] 日本語
Yorodumi
- PDB-8s8o: Solution Structure of cAMP-dependent Protein Kinase RII-alpha Sub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s8o
TitleSolution Structure of cAMP-dependent Protein Kinase RII-alpha Subunit Dimerization and Docking Domain Complex with Microtubule Associated Protein 2c (84-111)
Components
  • Isoform 3 of Microtubule-associated protein 2
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsPROTEIN BINDING / AKAP / PKA / MAP2c / IDP / protein-protein complex / 4-helix bundle / microtubule
Function / homology
Function and homology information


CA3 pyramidal cell dendrite / primary dendrite / apical distal dendrite / positive regulation of anterograde synaptic vesicle transport / positive regulation of anterograde dense core granule transport / regulation of organelle transport along microtubule / proximal neuron projection / dendritic filopodium / basal dendrite / distal dendrite ...CA3 pyramidal cell dendrite / primary dendrite / apical distal dendrite / positive regulation of anterograde synaptic vesicle transport / positive regulation of anterograde dense core granule transport / regulation of organelle transport along microtubule / proximal neuron projection / dendritic filopodium / basal dendrite / distal dendrite / cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / regulation of neurofibrillary tangle assembly / negative regulation of axon extension / dystroglycan binding / nucleotide-activated protein kinase complex / negative regulation of microtubule depolymerization / axon hillock / dendritic branch / proximal dendrite / axon initial segment / microtubule bundle formation / apical dendrite / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of microtubule polymerization / dendrite morphogenesis / establishment of cell polarity / ciliary base / protein kinase A catalytic subunit binding / central nervous system neuron development / dendritic growth cone / dendrite development / plasma membrane raft / PKA activation in glucagon signalling / DARPP-32 events / cAMP binding / Hedgehog 'off' state / dendrite cytoplasm / SH2 domain binding / axonogenesis / nuclear periphery / FCGR3A-mediated IL10 synthesis / response to progesterone / dendritic shaft / microtubule cytoskeleton organization / ruffle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron projection development / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / response to estradiol / actin cytoskeleton / regulation of protein localization / actin binding / Factors involved in megakaryocyte development and platelet production / microtubule cytoskeleton / cell body / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / microtubule binding / microtubule / calmodulin binding / neuron projection / postsynapse / postsynaptic density / intracellular signal transduction / protein domain specific binding / focal adhesion / neuronal cell body / ubiquitin protein ligase binding / dendrite / centrosome / protein kinase binding / glutamatergic synapse / protein-containing complex / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MAP2/Tau projection / MAP2/Tau projection 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 / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...MAP2/Tau projection / MAP2/Tau projection 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 / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / Microtubule-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / molecular dynamics / simulated annealing
AuthorsBartosik, V. / Lanikova, A. / Janackova, Z. / Padrta, P. / Zidek, L.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation20-12669S Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis of binding the unique N-terminal domain of microtubule-associated protein 2c to proteins regulating kinases of signaling pathways.
Authors: Bartosik, V. / Plucarova, J. / Lanikova, A. / Janackova, Z. / Padrta, P. / Jansen, S. / Varecka, V. / Gruber, T. / Feller, S.M. / Zidek, L.
History
DepositionMar 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: Isoform 3 of Microtubule-associated protein 2


Theoretical massNumber of molelcules
Total (without water)14,5953
Polymers14,5953
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 5789.617 Da / Num. of mol.: 2
Fragment: N-terminal docking and dimerization domain, residues 1-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR2A, PKR2, PRKAR2 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P13861
#2: Protein/peptide Isoform 3 of Microtubule-associated protein 2 / MAP-2


Mass: 3015.349 Da / Num. of mol.: 1 / Fragment: N-terminal PKA binding region, residues 80-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Map2, Mtap2 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P15146

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
132isotropic13D 1H-15N NOESY
142isotropic13D 1H-13C NOESY aliphatic
151isotropic13D 1H-15N NOESY filtered
161isotropic13D 1H-13C NOESY aliphatic filtered
172isotropic13D 1H-15N NOESY filtered
182isotropic13D 1H-13C NOESY aliphatic filtered
191isotropic12D 1H-15N HSQC
1122isotropic12D 1H-15N HSQC
1113anisotropic12D 1H-15N HSQC
1104isotropic12D 1H-15N HSQC
1143anisotropic12D 1H-15N HSQC IPAP
1134isotropic12D 1H-15N HSQC IPAP
1151isotropic13D HNCA
1161isotropic13D HN(CO)CA
1171isotropic13D HN(CA)CB
1181isotropic13D CBCA(CO)NH
1191isotropic33D (H)CCH-TOCSY
1205isotropic23D 1H-15N NOESY
1215isotropic23D 1H-13C NOESY aliphatic
1225isotropic33D (H)CCH-TOCSY
1232isotropic13D HNCA
1242isotropic13D HN(CO)CA
1252isotropic13D HN(CA)CB
1262isotropic13D CBCA(CO)NH
1272isotropic33D (H)CCH-TOCSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.5 mM [U-13C; U-15N] Microtubule associated protein 2c, 2 mM cAMP-dependent protein kinase type II-alpha regulatory subunit, 50 mM MOPS, 100 mM sodium chloride, 10 % v/v D2O, 17 mM sodium azide, 90% H2O/10% D2O(13C_15N)MAP2c_RIIDD90% H2O/10% D2O
solution20.56 mM Microtubule associated protein 2c, 1.12 mM [U-13C; U-15N] cAMP-dependent protein kinase type II-alpha regulatory subunit, 50 mM MOPS, 100 mM sodium chloride, 10 % v/v D2O, 10 mM sodium azide, 90% H2O/10% D2OMAP2c_(13C_15N)RIIDD90% H2O/10% D2O5mm tube
filamentous virus30.1 mM [U-15N] Microtubule associated protein 2c, 0.4 mM cAMP-dependent protein kinase type II-alpha regulatory subunit, 50 mM MOPS, 100 mM sodium chloride, 8 % v/v D2O, 40 mg/mL Pf1 phage, 90% H2O/10% D2O(15N)MAP2c_RIIDD_Pf190% H2O/10% D2O5mm tube
solution40.23 mM [U-15N] Microtubule associated protein 2c, 0.92 mM cAMP-dependent protein kinase type II-alpha regulatory subunit, 50 mM MOPS, 100 mM sodium chloride, 7.5 % v/v D2O, 90% H2O/10% D2O(15N)MAP2c_RIIDD_CTRL90% H2O/10% D2O5mm Shigemi tube
solution50.45 mM I,V-13C; I,L,V-15N Microtubule associated protein 2c, 1.8 mM cAMP-dependent protein kinase type II-alpha regulatory subunit, 50 mM MOPS, 100 mM sodium chloride, 7.5 % v/v D2O, 90% H2O/10% D2O(speclab)MAP2c_RIIDD90% H2O/10% D2O5mm Shigemi tube
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMicrotubule associated protein 2c[U-13C; U-15N]1
2 mMcAMP-dependent protein kinase type II-alpha regulatory subunitnatural abundance1
50 mMMOPSnatural abundance1
100 mMsodium chloridenatural abundance1
10 % v/vD2Onatural abundance1
17 mMsodium azidenatural abundance1
0.56 mMMicrotubule associated protein 2cnatural abundance2
1.12 mMcAMP-dependent protein kinase type II-alpha regulatory subunit[U-13C; U-15N]2
50 mMMOPSnatural abundance2
100 mMsodium chloridenatural abundance2
10 % v/vD2Onatural abundance2
10 mMsodium azidenatural abundance2
0.1 mMMicrotubule associated protein 2c[U-15N]3
0.4 mMcAMP-dependent protein kinase type II-alpha regulatory subunitnatural abundance3
50 mMMOPSnatural abundance3
100 mMsodium chloridenatural abundance3
8 % v/vD2Onatural abundance3
40 mg/mLPf1 phagenatural abundance3
0.23 mMMicrotubule associated protein 2c[U-15N]4
0.92 mMcAMP-dependent protein kinase type II-alpha regulatory subunitnatural abundance4
50 mMMOPSnatural abundance4
100 mMsodium chloridenatural abundance4
7.5 % v/vD2Onatural abundance4
0.45 mMMicrotubule associated protein 2cI,V-13C; I,L,V-15N5
1.8 mMcAMP-dependent protein kinase type II-alpha regulatory subunitnatural abundance5
50 mMMOPSnatural abundance5
100 mMsodium chloridenatural abundance5
7.5 % v/vD2Onatural abundance5
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 6.9 / Pressure: 1 bar / Temperature: 300.2 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9501
Bruker AVANCE III HDBrukerAVANCE III HD8502
Bruker AVANCE III HDBrukerAVANCE III HD6003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
NMRPipe11.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.115Goddardpeak picking
Sparky3.115Goddardchemical shift assignment
CYANA3.98.15Guntert, Mumenthaler and Wuthrichchemical shift assignment
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SCULPTOR3.1Charavay, Eynard, Hus, Bouvignies and Blackledgestructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SCULPTOR3.1Charavay, Eynard, Hus, Bouvignies and Blackledgerefinement
Refinement
MethodSoftware ordinalDetails
molecular dynamics1MDSA SCULPTOR-CNS TIP3P
simulated annealing2MDSA SCULPTOR-CNS TIP3P
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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