[English] 日本語
Yorodumi
- PDB-1a25: C2 DOMAIN FROM PROTEIN KINASE C (BETA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a25
TitleC2 DOMAIN FROM PROTEIN KINASE C (BETA)
ComponentsPROTEIN KINASE C (BETA)
KeywordsCALCIUM-BINDING PROTEIN / CALCIUM++/PHOSPHOLIPID BINDING PROTEIN
Function / homology
Function and homology information


dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / histone H3T6 kinase activity / Activation of NF-kappaB in B cells / VEGFR2 mediated cell proliferation / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin ...dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / histone H3T6 kinase activity / Activation of NF-kappaB in B cells / VEGFR2 mediated cell proliferation / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin / regulation of glucose transmembrane transport / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / negative regulation of glucose transmembrane transport / cellular response to carbohydrate stimulus / diacylglycerol-dependent serine/threonine kinase activity / response to vitamin D / presynaptic cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of growth / nuclear androgen receptor binding / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / B cell activation / Trafficking of GluR2-containing AMPA receptors / calcium channel regulator activity / calyx of Held / response to glucose / negative regulation of insulin receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / post-translational protein modification / protein kinase C binding / nuclear receptor coactivator activity / brush border membrane / B cell receptor signaling pathway / intracellular calcium ion homeostasis / positive regulation of insulin secretion / positive regulation of angiogenesis / calcium ion transport / histone binding / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / adaptive immune response / intracellular signal transduction / response to xenobiotic stimulus / phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. ...Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / C2 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
O-PHOSPHOETHANOLAMINE / Protein kinase C beta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSutton, R.B. / Sprang, S.R.
CitationJournal: Structure / Year: 1998
Title: Structure of the protein kinase Cbeta phospholipid-binding C2 domain complexed with Ca2+.
Authors: Sutton, R.B. / Sprang, S.R.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN KINASE C (BETA)
B: PROTEIN KINASE C (BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1769
Polymers33,7642
Non-polymers4127
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-77 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.798, 77.798, 140.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.912012, 0.409902, -0.014639), (0.410099, 0.910658, -0.050199), (-0.007246, -0.051786, -0.998632)
Vector: -16.5808, 4.693, 41.7363)

-
Components

#1: Protein PROTEIN KINASE C (BETA) / CALB


Mass: 16882.111 Da / Num. of mol.: 2 / Fragment: CALCIUM/PHOSPHOLIPID BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P68403, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PSE / O-PHOSPHOETHANOLAMINE


Mass: 171.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10NO5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG1500, 100 MM MES, PH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %(w/v)PEG15001drop
22 mM1dropCaCl2
32 mMo-phospho-L-serine1drop
4100 mMMES1drop

-
Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 12297 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8 / Rsym value: 0.26 / % possible all: 95

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RSY

1rsy


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1365552.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT TARGET FUNCTION : MLF DATA CUTOFF HIGH (ABS(F)) : 1365552.04 DATA CUTOFF LOW (ABS(F)) : 0.000000
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1254 10.3 %RANDOM
Rwork0.222 ---
obs0.222 12233 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2---3.61 Å20 Å2
3---7.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 16 49 2241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.371.5
X-RAY DIFFRACTIONc_mcangle_it5.222
X-RAY DIFFRACTIONc_scbond_it5.832
X-RAY DIFFRACTIONc_scangle_it8.042.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 182 9.4 %
Rwork0.355 1759 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PSE.PARPSE.TOP
X-RAY DIFFRACTION3PARCAL.PROTOPCAL.PRO
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.2 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

+
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