[English] 日本語
Yorodumi
- PDB-2drn: Docking and dimerization domain (D/D) of the Type II-alpha regula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2drn
TitleDocking and dimerization domain (D/D) of the Type II-alpha regulatory subunity of protein kinase A (PKA) in complex with a peptide from an A-kinase anchoring protein
Components
  • 24-residues peptide from an a-kinase anchoring protein
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsTRANSFERASE / AKAP / PKA / signal transduction / 4-helix bundle / helix-loop-helix / protein-peptide complex
Function / homology
Function and homology information


regulation of glucocorticoid mediated signaling pathway / regulation of sarcomere organization / guanyl-nucleotide exchange factor activity => GO:0005085 / GPER1 signaling / small GTPase binding => GO:0031267 / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process ...regulation of glucocorticoid mediated signaling pathway / regulation of sarcomere organization / guanyl-nucleotide exchange factor activity => GO:0005085 / GPER1 signaling / small GTPase binding => GO:0031267 / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / : / Hedgehog 'off' state / PKA activation / cell growth involved in cardiac muscle cell development / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / MAP-kinase scaffold activity / cardiac muscle cell differentiation / regulation of Rho protein signal transduction / Vasopressin regulates renal water homeostasis via Aquaporins / nuclear export / regulation of small GTPase mediated signal transduction / cAMP-dependent protein kinase inhibitor activity / protein kinase A binding / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / RHOB GTPase cycle / positive regulation of Rho protein signal transduction / adrenergic receptor signaling pathway / NRAGE signals death through JNK / RHOC GTPase cycle / plasma membrane raft / protein kinase A catalytic subunit binding / RHOA GTPase cycle / small molecule binding / beta-2 adrenergic receptor binding / cAMP binding / T-tubule / guanyl-nucleotide exchange factor activity / actin filament / regulation of protein phosphorylation / positive regulation of MAP kinase activity / modulation of chemical synaptic transmission / bone development / small GTPase binding / G alpha (12/13) signalling events / actin cytoskeleton / heart development / cell cortex / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / protein domain specific binding / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / synapse / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
A-kinase anchor protein 13 / RII binding domain / RII binding domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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 / ARHGEF1-like, PH domain ...A-kinase anchor protein 13 / RII binding domain / RII binding domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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 / ARHGEF1-like, PH domain / PH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / C1-like domain superfamily / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / RmlC-like jelly roll fold / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / A-kinase anchor protein 13 / A-kinase anchor protein 13
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsNewlon, M.G. / Roy, M. / Morikis, D. / Hausken, Z.E. / Coghlan, V. / Scott, J.D. / Jennings, P.A.
CitationJournal: Embo J. / Year: 2001
Title: A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes.
Authors: Newlon, M.G. / Roy, M. / Morikis, D. / Carr, D.W. / Westphal, R. / Scott, J.D. / Jennings, P.A.
History
DepositionJun 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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: 24-residues peptide from an a-kinase anchoring protein


Theoretical massNumber of molelcules
Total (without water)13,3303
Polymers13,3303
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 5398.181 Da / Num. of mol.: 2
Fragment: N-terminal docking and dimerization domain, residues 4-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RIIA(1-44) / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / References: UniProt: P12368, EC: 2.7.1.37
#2: Protein/peptide 24-residues peptide from an a-kinase anchoring protein / Fragment / Human thyroid anchoring protein / Ht31(493-515) peptide


Mass: 2533.828 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide has been generated by solid phase peptide synthesis.; This sequence occurs naturally in humans.
References: UniProt: Q14572, UniProt: Q12802*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: This structure was determined using standard 2d and 3d heteronuclear and homonuclear techniques.

-
Sample preparation

DetailsContents: 2mM RII-alpha(1-44); 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851brungerstructure solution
X-PLOR3.851brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1370 restraints, 1247 are noe-derived distance restraints, 50 dihedral angle restraints,73 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 13

+
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://pdbjlvh1.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