[English] 日本語
Yorodumi
- PDB-5kjx: Co-crystal Structure of PKA RI alpha CNB-B domain with cAMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kjx
TitleCo-crystal Structure of PKA RI alpha CNB-B domain with cAMP
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsSIGNALING PROTEIN / Cyclic nucleotide / cAMP-dependent protein kinase / Nucleotide selectivity / Cyclic nucleotide binding domain
Function / homology
Function and homology information


activation of protein kinase A activity / cAMP-dependent protein kinase regulator activity / ALK mutants bind TKIs / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of activated T cell proliferation / ciliary base ...activation of protein kinase A activity / cAMP-dependent protein kinase regulator activity / ALK mutants bind TKIs / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of activated T cell proliferation / ciliary base / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / sperm head-tail coupling apparatus / plasma membrane raft / DARPP-32 events / cAMP binding / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / negative regulation of cAMP/PKA signal transduction / Hedgehog 'off' state / multivesicular body / cellular response to glucagon stimulus / FCGR3A-mediated IL10 synthesis / neuromuscular junction / negative regulation of inflammatory response to antigenic stimulus / Signaling by ALK fusions and activated point mutants / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / adenylate cyclase-activating G protein-coupled receptor signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / chemical synaptic transmission / intracellular signal transduction / protein domain specific binding / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / centrosome / glutamatergic synapse / protein-containing complex / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding 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 / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLorenz, R. / Moon, E. / Kim, J.J. / Huang, G.Y. / Kim, C. / Herberg, F.W.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
Federal Ministry of Education and Research GrantFKZ 0316177F (No Pain) Germany
the Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) of the University of Kassel Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM090161-06 United States
CitationJournal: Biochem. J. / Year: 2017
Title: Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity.
Authors: Lorenz, R. / Moon, E.W. / Kim, J.J. / Schmidt, S.H. / Sankaran, B. / Pavlidis, I.V. / Kim, C. / Herberg, F.W.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2862
Polymers16,9571
Non-polymers3291
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.897, 52.207, 74.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer according to gel filtration

-
Components

#1: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit / Tissue-specific extinguisher 1 / TSE1


Mass: 16956.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1A, PKR1, PRKAR1, TSE1 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): TP2000 (delta cya) / References: UniProt: P10644
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% w/v PEG 8000, 100mM imidazole/hydrochloric acid pH 6.5, 3% v/v MPD

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→24.65 Å / Num. obs: 11873 / % possible obs: 97.08 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 50.71
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.5 / % possible all: 74.4

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGS

1rgs


Resolution: 1.9→24.646 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2263 600 5.05 %
Rwork0.1784 --
obs0.1808 11873 97.13 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 34.299 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.8016 Å20 Å20 Å2
2--5.5833 Å2-0 Å2
3---3.2184 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 22 115 1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071119
X-RAY DIFFRACTIONf_angle_d1.1231519
X-RAY DIFFRACTIONf_dihedral_angle_d15.115415
X-RAY DIFFRACTIONf_chiral_restr0.074173
X-RAY DIFFRACTIONf_plane_restr0.004194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8995-2.09060.23871380.20092519X-RAY DIFFRACTION88
2.0906-2.39290.26781500.17362844X-RAY DIFFRACTION100
2.3929-3.01390.2551510.1852878X-RAY DIFFRACTION100
3.0139-24.64850.20381610.17383032X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.93552.4552-2.0118.0549-4.61082.9486-0.6941.80790.3186-1.2030.82260.61250.3947-0.1071-0.00410.4801-0.0681-0.06850.54040.04990.27381.5132-6.4986-20.4286
24.5437-1.04821.69516.32281.61666.5450.2777-0.04120.1614-0.09280.47111.2117-0.4927-1.1286-0.55120.34640.00510.04770.38070.23090.5712-7.4482-0.6435-13.7935
33.5445-5.20575.01639.0426-8.32429.15240.04740.36940.3009-0.4424-0.20940.06-0.11290.3550.08940.2746-0.0475-0.05720.22650.0760.26922.10730.6136-18.4006
44.3353-0.45150.16813.415-0.28613.78390.0811-0.42070.07420.063-0.1339-0.1929-0.19320.35250.01680.1309-0.0452-0.00570.17670.02310.13444.3278-9.9479-1.3416
50.1124-1.06150.59532.0004-3.81134.5543-0.1575-1.87520.03372.1979-0.1055-0.7398-0.53861.2757-0.00490.5275-0.08820.02041.0135-0.0440.2756-0.4174-7.457715.9151
64.02560.8919-0.35443.7987-0.90793.73770.1227-0.59950.25590.3566-0.06150.0561-0.33920.039-0.07640.15930.00230.02530.2131-0.02630.1436-0.8909-5.78012.1551
77.13123.55410.01766.4694-1.59084.78480.05630.11710.3650.1464-0.1265-0.3876-0.3510.38180.13690.1757-0.0055-0.02740.20910.0030.17676.3537-3.5132-8.18
85.74670.915-3.67563.2611-1.47238.39490.226-0.23941.02680.3883-0.05510.8897-1.2646-0.5921-0.24760.35540.0495-0.02680.2047-0.09030.5158-4.75614.2044-0.8534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 239:250)
2X-RAY DIFFRACTION2chain 'A' and (resseq 251:258)
3X-RAY DIFFRACTION3chain 'A' and (resseq 259:274)
4X-RAY DIFFRACTION4chain 'A' and (resseq 275:302)
5X-RAY DIFFRACTION5chain 'A' and (resseq 303:310)
6X-RAY DIFFRACTION6chain 'A' and (resseq 311:342)
7X-RAY DIFFRACTION7chain 'A' and (resseq 343:356)
8X-RAY DIFFRACTION8chain 'A' and (resseq 357:379)

+
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