[English] 日本語
Yorodumi
- PDB-2i0e: Structure of catalytic domain of human protein kinase C beta II c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i0e
TitleStructure of catalytic domain of human protein kinase C beta II complexed with a bisindolylmaleimide inhibitor
ComponentsProtein Kinase C-beta II
KeywordsTRANSFERASE / Protein Kinase C Beta II / Protein Kinase C / Serine/Threonine Protein Kinase
Function / homology
Function and homology information


dibenzo-p-dioxin metabolic process / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / histone H3T6 kinase activity / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin / regulation of glucose transmembrane transport / Depolymerization of the Nuclear Lamina / Trafficking of GluR2-containing AMPA receptors ...dibenzo-p-dioxin metabolic process / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / histone H3T6 kinase activity / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin / regulation of glucose transmembrane transport / Depolymerization of the Nuclear Lamina / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / 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 / mitotic nuclear membrane disassembly / response to vitamin D / presynaptic cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / regulation of growth / lipoprotein transport / nuclear androgen receptor binding / regulation of synaptic vesicle exocytosis / B cell activation / regulation of dopamine secretion / calyx of Held / calcium channel regulator activity / RHO GTPases Activate NADPH Oxidases / response to glucose / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / post-translational protein modification / nuclear receptor coactivator activity / VEGFR2 mediated cell proliferation / protein kinase C binding / Activation of NF-kappaB in B cells / brush border membrane / B cell receptor signaling pathway / positive regulation of insulin secretion / intracellular calcium ion homeostasis / G alpha (z) signalling events / 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 / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type profile. ...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 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PDS / Protein kinase C beta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGrodsky, N.B. / Love, R.L.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of the Catalytic Domain of Human Protein Kinase C beta II Complexed with a Bisindolylmaleimide Inhibitor
Authors: Grodsky, N. / Li, Y. / Bouzida, D. / Love, R. / Jensen, J. / Nodes, B. / Nonomiya, J. / Grant, S.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE ACCORDING TO THE AUTHORS OF THE ENTRY, CONFLICTS ARISE BETWEEN THEIR SEQUENCE AND THE UNP ... SEQUENCE ACCORDING TO THE AUTHORS OF THE ENTRY, CONFLICTS ARISE BETWEEN THEIR SEQUENCE AND THE UNP REFERENCE SEQUENCE BECAUSE THEIR SEQUENCE IS OF PKC-BETAII AND THE UNP REFERENCE SEQUENCE IS OF PKC-BETAI.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Kinase C-beta II
B: Protein Kinase C-beta II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4744
Polymers81,5932
Non-polymers8812
Water2,072115
1
A: Protein Kinase C-beta II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2372
Polymers40,7961
Non-polymers4411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Kinase C-beta II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2372
Polymers40,7961
Non-polymers4411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Protein Kinase C-beta II
hetero molecules

A: Protein Kinase C-beta II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4744
Polymers81,5932
Non-polymers8812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area4180 Å2
ΔGint-16 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.098, 131.417, 83.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Protein Kinase C-beta II


Mass: 40796.359 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, residues 321-673
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcSG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P05771, protein kinase C
#2: Chemical ChemComp-PDS / 3-{1-[3-(DIMETHYLAMINO)PROPYL]-2-METHYL-1H-INDOL-3-YL}-4-(2-METHYL-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE


Mass: 440.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H28N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M ADA, 2.5 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 4, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 32375 / Num. obs: 32375 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 28.4
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.484 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Akt-1

Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.644 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.438 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28973 670 2.1 %RANDOM
Rwork0.23542 ---
obs0.23654 31651 99.9 %-
all-32375 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.9 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 66 115 5293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225318
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9887187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24324.502251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75615.032928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4871522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024043
X-RAY DIFFRACTIONr_nbd_refined0.2140.22383
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.23
X-RAY DIFFRACTIONr_mcbond_it0.5561.53218
X-RAY DIFFRACTIONr_mcangle_it0.99625058
X-RAY DIFFRACTIONr_scbond_it1.05532424
X-RAY DIFFRACTIONr_scangle_it1.7474.52129
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 50 -
Rwork0.338 2255 -
obs--98.72 %

+
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