[English] 日本語
Yorodumi
- PDB-1atp: 2.2 angstrom refined crystal structure of the catalytic subunit o... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1atp
Title2.2 angstrom refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MNATP and a peptide inhibitor
Components
  • PEPTIDE INHIBITOR PKI(5-24)
  • cAMP-DEPENDENT PROTEIN KINASEProtein kinase A
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homologyDARPP-32 events / AGC-kinase, C-terminal / Interleukin-3, Interleukin-5 and GM-CSF signaling / Protein kinase-like domain superfamily / VEGFA-VEGFR2 Pathway / Serine/threonine-protein kinase, active site / cAMP-dependent protein kinase inhibitor / Vasopressin regulates renal water homeostasis via Aquaporins / Protein kinase domain / Protein kinase domain ...DARPP-32 events / AGC-kinase, C-terminal / Interleukin-3, Interleukin-5 and GM-CSF signaling / Protein kinase-like domain superfamily / VEGFA-VEGFR2 Pathway / Serine/threonine-protein kinase, active site / cAMP-dependent protein kinase inhibitor / Vasopressin regulates renal water homeostasis via Aquaporins / Protein kinase domain / Protein kinase domain / Regulation of insulin secretion / Rap1 signalling / Loss of Nlp from mitotic centrosomes / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Recruitment of NuMA to mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Regulation of PLK1 Activity at G2/M Transition / cAMP-dependent protein kinase catalytic subunit alpha / Protein kinase, ATP binding site / Ion homeostasis / AURKA Activation by TPX2 / PKA activation / AGC-kinase C-terminal domain profile. / Protein kinase domain profile. / HDL assembly / Serine/Threonine protein kinases active-site signature. / GLI3 is processed to GLI3R by the proteasome / Protein kinases ATP-binding region signature. / Factors involved in megakaryocyte development and platelet production / RET signaling / MAPK6/MAPK4 signaling / CD209 (DC-SIGN) signaling / Anchoring of the basal body to the plasma membrane / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor / PKA activation in glucagon signalling / calcium-dependent protein kinase activity / negative regulation of meiotic cell cycle / regulation of cellular respiration / sperm midpiece / nucleotide-activated protein kinase complex / negative regulation of protein import into nucleus / negative regulation of cAMP-dependent protein kinase activity / cAMP-dependent protein kinase inhibitor activity / negative regulation of catalytic activity / cAMP-dependent protein kinase / regulation of protein processing / negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase activity / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / ciliary base / protein kinase A regulatory subunit binding / sperm capacitation / protein kinase A signaling / axoneme / sperm flagellum / mesoderm formation / regulation of osteoblast differentiation / plasma membrane raft / intercellular bridge / Rab GTPase binding / protein kinase A catalytic subunit binding / regulation of synaptic transmission, glutamatergic / acrosomal vesicle / positive regulation of cell cycle arrest / regulation of proteasomal protein catabolic process / negative regulation of protein kinase activity / cellular response to glucose stimulus / neural tube closure / protein serine/threonine/tyrosine kinase activity / positive regulation of protein export from nucleus / modulation of chemical synaptic transmission / neuromuscular junction / mRNA processing / regulation of G2/M transition of mitotic cell cycle / cellular response to heat / peptidyl-threonine phosphorylation / manganese ion binding / dendritic spine / peptidyl-serine phosphorylation / protein-containing complex binding / nuclear speck / neuron projection / protein kinase activity / centrosome / protein autophosphorylation / protein domain specific binding / ubiquitin protein ligase binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / protein kinase binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / protein-containing complex
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodX-RAY DIFFRACTION / 2.2 Å resolution
AuthorsZheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Teneyck, L.F. / Sowadski, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: 2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.
Authors: Zheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N.H. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M.
#1: Journal: To be Published
Title: 2.0 Angstrom Refined Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with a Peptide Inhibitor and Detergent
Authors: Knighton, D.R. / Bell, S.M. / Zheng, J. / Teneyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#2: Journal: Biochemistry / Year: 1993
Title: Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mg/ATP and Peptide Inhibitor
Authors: Zheng, J. / Knighton, D.R. / Teneyck, L.F. / Karlsson, R. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#3: Journal: Science / Year: 1991
Title: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Authors: Knighton, D.R. / Zheng, J. / Teneyck, L.F. / Xuong, V.A. / Ashford, N.-H. / Taylor, S.S. / Sowadski, J.M.
#4: Journal: Science / Year: 1991
Title: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Authors: Knighton, D.R. / Zheng, J. / Teneyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#5: Journal: J.Biol.Chem. / Year: 1989
Title: Expression of the Catalytic Subunit of C/AMP-Dependent Protein Kinase in Escherichia Coli
Authors: Slice, L.W. / Taylor, S.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 8, 1993 / Release: Apr 15, 1993
RevisionDateData content typeGroupProviderType
1.0Apr 15, 1993Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: cAMP-DEPENDENT PROTEIN KINASE
I: PEPTIDE INHIBITOR PKI(5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5015
Polyers42,8842
Non-polymers6173
Water1,856103
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3770
ΔGint (kcal/M)-14
Surface area (Å2)15170
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)73.580, 76.280, 80.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21
Atom site foot note1: RESIDUES THR E 197 AND SER E 338 ARE PHOSPHORYLATED.

-
Components

#1: Protein/peptide cAMP-DEPENDENT PROTEIN KINASE / Protein kinase A


Mass: 40657.316 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus (house mouse) / Genus: Mus / References: UniProt: P05132, EC: 2.7.1.37
#2: Protein/peptide PEPTIDE INHIBITOR PKI(5-24)


Mass: 2226.411 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus (house mouse) / Genus: Mus / References: UniProt: P63248
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Formula: Mn / Manganese
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Formula: H2O / Water
Nonpolymer detailsINHIBITOR RESIDUE NUMBERING CORRESPONDS TO NUMBERS FROM THE SEQUENCE OF THE LARGER NATURALLY ...INHIBITOR RESIDUE NUMBERING CORRESPONDS TO NUMBERS FROM THE SEQUENCE OF THE LARGER NATURALLY OCCURRING PKI PROTEIN OF WHICH THE INHIBITOR IS A SYNTHETIC FRAGMENT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.65 / Density percent sol: 53.51 %
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Zheng, J., (1993) Biochemistry, 32, 2154.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mg/mlprotein1drop
250 mMBicine1drop
3150 mMammonium acetate1drop
410 mMdithiothreitol1drop
58 %(w/v)PEG4001drop
610 mMdithiothreitol1reservoir
78 %(w/v)PEG4001reservoir
815 %methanol1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.2 / Number obs: 21443 / Percent possible obs: 90.6 / Rmerge I obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.2 / Lowest resolution: 2.37 / Rmerge I obs: 0.079

-
Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefineSigma F: 2
Least-squares processR factor R work: 0.177 / Highest resolution: 2.2 / Lowest resolution: 10
Refine hist #LASTHighest resolution: 2.2 / Lowest resolution: 10
Number of atoms included #LASTProtein: 2934 / Nucleic acid: 0 / Ligand: 33 / Solvent: 103 / Total: 3070
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.2
Software
*PLUS
Name: XPLOR/TNT / Classification: refinement
Least-squares process
*PLUS
R factor all: 0.199 / R factor obs: 0.177
Refine LS restraints
*PLUS
Refine IDType
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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