[English] 日本語
Yorodumi
- PDB-3shr: Crystal Structure of cGMP-dependent Protein Kinase Reveals Novel ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3shr
TitleCrystal Structure of cGMP-dependent Protein Kinase Reveals Novel Site of Interchain Communication
ComponentscGMP-dependent protein kinase 1
KeywordsTRANSFERASE / cyclic nucleotide binding domains / cyclic nucleotide protein kinase / PKG / cGMP-dependent protein kinase
Function / homology
Function and homology information


cGMP effects / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / Rap1 signalling / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle / regulation of GTPase activity / cGMP-mediated signaling ...cGMP effects / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / Rap1 signalling / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle / regulation of GTPase activity / cGMP-mediated signaling / dendrite development / negative regulation of vascular associated smooth muscle cell proliferation / cGMP binding / calcium channel regulator activity / forebrain development / protein kinase A signaling / neuron migration / protein serine kinase activity / Golgi apparatus / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Jelly Rolls / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOsborne, B.W. / Wu, J. / Taylor, S.S. / Dostmann, W.R.
CitationJournal: Structure / Year: 2011
Title: Crystal Structure of cGMP-Dependent Protein Kinase Reveals Novel Site of Interchain Communication.
Authors: Osborne, B.W. / Wu, J. / McFarland, C.J. / Nickl, C.K. / Sankaran, B. / Casteel, D.E. / Woods, V.L. / Kornev, A.P. / Taylor, S.S. / Dostmann, W.R.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cGMP-dependent protein kinase 1
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2116
Polymers67,3612
Non-polymers8514
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-54 kcal/mol
Surface area29290 Å2
MethodPISA
2
A: cGMP-dependent protein kinase 1
B: cGMP-dependent protein kinase 1
hetero molecules

A: cGMP-dependent protein kinase 1
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,42312
Polymers134,7224
Non-polymers1,7018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area6050 Å2
ΔGint-34 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.156, 66.039, 81.550
Angle α, β, γ (deg.)90.00, 113.84, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein cGMP-dependent protein kinase 1 / cGK 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


Mass: 33680.465 Da / Num. of mol.: 2 / Fragment: unp residues 79-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Production host: Escherichia coli (E. coli) / References: UniProt: P00516, cGMP-dependent protein kinase
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 2.2M (NH4)2SO4, 100mM Tris, 0.2% MPD at a protein concentration of 25-35 mg/mL , pH 8.0, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32166 / % possible obs: 97.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.7
Reflection shellResolution: 2.49→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / % possible all: 93.5

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RGS

1rgs


Resolution: 2.5→50 Å
RfactorNum. reflection
Rfree0.277 -
Rwork0.221 -
obs0.221 25428
all-32166
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 54 0 4277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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