[English] 日本語
Yorodumi
- PDB-5h78: Crystal structure of the PKA-DHR14 fusion protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h78
TitleCrystal structure of the PKA-DHR14 fusion protein
ComponentscAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14
KeywordsSIGNALING PROTEIN / DE NOVO PROTEIN / synthetic protein
Function / homology
Function and homology information


cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / nucleotide-activated protein kinase complex / 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 / ciliary base / protein kinase A catalytic subunit binding ...cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / nucleotide-activated protein kinase complex / 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 / ciliary base / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / DARPP-32 events / cAMP binding / Hedgehog 'off' state / FCGR3A-mediated IL10 synthesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / intracellular signal transduction / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / centrosome / protein-containing complex / extracellular exosome / 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 / RmlC-like jelly roll fold
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsYoun, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.
CitationJournal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.
History
DepositionNov 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 II-alpha regulatory subunit,DHR14
B: cAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14


Theoretical massNumber of molelcules
Total (without water)44,6672
Polymers44,6672
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-18 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.234, 96.539, 39.351
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

-
Components

#1: Protein cAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14


Mass: 22333.561 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-40 (UNP RESIDUES 5-41),RESIDUES 41-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: PRKAR2A, PKR2, PRKAR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13861
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.91 Å3/Da / Density % sol: 68.51 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: 0.05M sodium cacodylate pH 6.5, 0.01M magnesium chloride, 0.2M potassium chloride, 12%(w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 83181 / % possible obs: 98.7 % / Redundancy: 3.5 % / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.21 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZX, 5CWH

2izx

5cwh


Resolution: 2.002→29.593 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.52
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2068 3689 4.43 %
Rwork0.181 --
obs0.1822 83181 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→29.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 0 445 3505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093080
X-RAY DIFFRACTIONf_angle_d0.8574156
X-RAY DIFFRACTIONf_dihedral_angle_d22.2551976
X-RAY DIFFRACTIONf_chiral_restr0.051520
X-RAY DIFFRACTIONf_plane_restr0.005528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0018-2.02820.24061310.24572687X-RAY DIFFRACTION83
2.0282-2.05590.2891110.23173057X-RAY DIFFRACTION90
2.0559-2.08530.27331470.21772994X-RAY DIFFRACTION92
2.0853-2.11640.19371020.21512987X-RAY DIFFRACTION92
2.1164-2.14950.22421310.19913018X-RAY DIFFRACTION92
2.1495-2.18470.22811460.18933127X-RAY DIFFRACTION92
2.1847-2.22240.1731640.17692937X-RAY DIFFRACTION93
2.2224-2.26280.19121320.18493020X-RAY DIFFRACTION93
2.2628-2.30630.17211070.18563099X-RAY DIFFRACTION92
2.3063-2.35330.25481570.18722977X-RAY DIFFRACTION94
2.3533-2.40450.21041310.18383081X-RAY DIFFRACTION94
2.4045-2.46040.20871720.17643078X-RAY DIFFRACTION93
2.4604-2.52190.23581370.17963044X-RAY DIFFRACTION95
2.5219-2.590.23171570.17613065X-RAY DIFFRACTION94
2.59-2.66620.22991460.16583083X-RAY DIFFRACTION95
2.6662-2.75220.18521370.17633119X-RAY DIFFRACTION95
2.7522-2.85050.15841560.17653051X-RAY DIFFRACTION95
2.8505-2.96450.23181350.16643174X-RAY DIFFRACTION96
2.9645-3.09930.2121820.18783104X-RAY DIFFRACTION96
3.0993-3.26250.19911340.18323128X-RAY DIFFRACTION96
3.2625-3.46660.18981520.16573170X-RAY DIFFRACTION96
3.4666-3.73380.19011270.15853123X-RAY DIFFRACTION96
3.7338-4.10870.18881500.16073131X-RAY DIFFRACTION96
4.1087-4.70120.18511370.15253171X-RAY DIFFRACTION96
4.7012-5.91520.22861550.19173189X-RAY DIFFRACTION98
5.9152-29.59590.21541530.23452878X-RAY DIFFRACTION88
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)
17.61412.62620.28627.0261-1.94797.34490.0753-0.39090.08360.5071-0.1986-0.2716-0.19450.16490.11260.14440.0464-0.00330.2755-0.050.2877-4.3718-52.42715.2097
23.9089-5.3472-4.31127.27725.88964.7476-0.2607-0.303-0.04210.41230.4677-0.33530.1710.3644-0.230.15460.0513-0.03850.296-0.0190.2482-17.4174-42.83819.9165
33.39460.28270.29331.32580.19111.8876-0.00560.0641-0.1015-0.01820.0252-0.09570.08820.1969-0.00530.14410.0280.00950.10980.0130.0619-37.0792-32.248619.2871
42.445-2.3784-1.79446.4654.72235.3594-0.0529-0.0767-0.2410.0983-0.08340.24510.3642-0.33040.07760.1572-0.05070.01560.16450.01650.1176-55.5472-36.811920.7794
53.76353.18271.57033.1781.35651.0155-0.06340.1070.0612-0.10540.119-0.19260.01620.1239-0.03760.14220.00010.02330.2121-0.00860.1559-19.0225-60.15730.656
62.8142-0.03450.11281.79710.75262.1096-0.03010.01360.1658-0.0046-0.0010.0745-0.2097-0.09750.030.1519-0.0142-0.00410.09690.02510.0575-47.9324-66.640.2823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 196 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 97 )
6X-RAY DIFFRACTION6chain 'B' and (resid 98 through 196 )

+
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