[English] 日本語
Yorodumi
- PDB-2hwn: Crystal Structure of RII alpha Dimerization/Docking domain of PKA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hwn
TitleCrystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide
Components
  • A Kinase binding peptide
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsTRANSFERASE / PKA / AKAP / Dimerization/Docking / D/D / Regulatory Subunit
Function / homology
Function and homology information


GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / Hedgehog 'off' state / PKA activation / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins ...GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / Hedgehog 'off' state / PKA activation / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / cAMP-dependent protein kinase inhibitor activity / protein kinase A binding / cAMP-dependent protein kinase complex / plasma membrane raft / protein kinase A catalytic subunit binding / small molecule binding / beta-2 adrenergic receptor binding / cAMP binding / T-tubule / regulation of protein phosphorylation / modulation of chemical synaptic transmission / kinase activity / 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 / plasma membrane / cytoplasm / cytosol
Similarity search - Function
A-kinase anchor protein 10, PKA-binding (AKB) 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 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. ...A-kinase anchor protein 10, PKA-binding (AKB) 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 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / Testis cDNA, clone: QtsA-21406, similar to human A kinase (PRKA) anchor protein 10 (AKAP10), nuclear geneencoding mitochondrial protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKinderman, F. / Kim, C.
CitationJournal: Mol.Cell / Year: 2006
Title: A Dynamic Mechanism for AKAP Binding to RII Isoforms of cAMP-Dependent Protein Kinase.
Authors: Kinderman, F.S. / Kim, C. / von Daake, S. / Ma, Y. / Pham, B.Q. / Spraggon, G. / Xuong, N.H. / Jennings, P.A. / Taylor, S.S.
History
DepositionAug 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: cAMP-dependent protein kinase type II-alpha regulatory subunit
E: A Kinase binding peptide
F: A Kinase binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4757
Polymers26,3836
Non-polymers921
Water3,801211
1
A: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
E: A Kinase binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2834
Polymers13,1913
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-40 kcal/mol
Surface area6130 Å2
MethodPISA
2
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: cAMP-dependent protein kinase type II-alpha regulatory subunit
F: A Kinase binding peptide


Theoretical massNumber of molelcules
Total (without water)13,1913
Polymers13,1913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-35 kcal/mol
Surface area5990 Å2
MethodPISA
3
A: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
E: A Kinase binding peptide
hetero molecules

C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: cAMP-dependent protein kinase type II-alpha regulatory subunit
F: A Kinase binding peptide


Theoretical massNumber of molelcules
Total (without water)26,4757
Polymers26,3836
Non-polymers921
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8730 Å2
ΔGint-88 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.551, 44.561, 72.802
Angle α, β, γ (deg.)90.00, 124.07, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is one of the two dimers.

-
Components

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


Mass: 5290.060 Da / Num. of mol.: 4 / Fragment: Dimerization/docking domain, residues 0-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkar2a / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12368, cAMP-dependent protein kinase
#2: Protein/peptide A Kinase binding peptide


Mass: 2611.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: Q4R5S0*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2005
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→35.5 Å / Num. all: 30976 / Num. obs: 29191 / % possible obs: 87.65 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 36.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3523 / Rsym value: 0.396 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.014 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1607 5.2 %RANDOM
Rwork0.208 ---
all0.2098 30976 --
obs0.20823 29191 87.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20.82 Å2
2---0.54 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 6 211 1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221673
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9992279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7535200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74723.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12115272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1371514
X-RAY DIFFRACTIONr_chiral_restr0.120.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021270
X-RAY DIFFRACTIONr_nbd_refined0.2080.2852
X-RAY DIFFRACTIONr_nbtor_refined0.310.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.216
X-RAY DIFFRACTIONr_mcbond_it0.8971.51068
X-RAY DIFFRACTIONr_mcangle_it1.36621680
X-RAY DIFFRACTIONr_scbond_it2.0373684
X-RAY DIFFRACTIONr_scangle_it3.0254.5599
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 132 -
Rwork0.28 2461 -
obs-2593 99.92 %
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)
12.96341.58260.41462.1701-0.92362.18710.1168-0.12780.09280.1984-0.06920.2428-0.0026-0.1905-0.0477-0.3354-0.003-0.0037-0.2551-0.0331-0.275-16.842-23.6883.764
25.95972.7481-1.89231.5114-1.12780.8676-0.07930.2158-0.2594-0.10540.0270.02990.1117-0.02950.0523-0.2749-0.0247-0.019-0.2189-0.0184-0.1853-18.781-31.0050.243
31.37670.418-0.03943.20541.92133.25830.0884-0.21490.12490.3446-0.160.3230.0624-0.26380.0716-0.2282-0.02850.0093-0.2109-0.0177-0.3122-1.959-19.22624.19
40.4849-0.1453-0.02982.90913.28715.24340.006-0.02220.03880.1184-0.02640.0804-0.2030.02230.0203-0.2208-0.0218-0.0035-0.2544-0.0137-0.31182.12-12.16224.631
511.28446.72552.249711.43683.56538.5128-0.21940.69490.1521-0.43470.24060.42570.0216-0.3409-0.0212-0.3180.0185-0.0357-0.13030.0245-0.2505-15.971-20.446-9.414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 43
2X-RAY DIFFRACTION2B3 - 44
3X-RAY DIFFRACTION3C8 - 43
4X-RAY DIFFRACTION4D3 - 43
5X-RAY DIFFRACTION5E2 - 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://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