[English] 日本語
Yorodumi
- PDB-9s9t: Structure of human PKCBeta Kinase domain with Ruboxistaurin, D427... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s9t
TitleStructure of human PKCBeta Kinase domain with Ruboxistaurin, D427N mutant
ComponentsIsoform Beta-II of Protein kinase C beta type
KeywordsTRANSFERASE / Kinase / Inhibitor / Mutant
Function / homology
Function and homology information


Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / cellular response to carbohydrate stimulus / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C signaling / histone H3T6 kinase activity / spectrin / regulation of D-glucose transmembrane transport / Trafficking of GluR2-containing AMPA receptors / Depolymerization of the Nuclear Lamina ...Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / cellular response to carbohydrate stimulus / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C signaling / histone H3T6 kinase activity / spectrin / regulation of D-glucose transmembrane transport / Trafficking of GluR2-containing AMPA receptors / Depolymerization of the Nuclear Lamina / WNT5A-dependent internalization of FZD4 / negative regulation of D-glucose transmembrane transport / protein kinase C / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / mitotic nuclear membrane disassembly / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of vascular endothelial growth factor receptor signaling pathway / lipoprotein transport / nuclear androgen receptor binding / regulation of synaptic vesicle exocytosis / B cell activation / RHO GTPases Activate NADPH Oxidases / presynaptic cytosol / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / protein kinase C binding / calyx of Held / VEGFR2 mediated cell proliferation / B cell receptor signaling pathway / calcium channel regulator activity / Activation of NF-kappaB in B cells / positive regulation of insulin secretion / positive regulation of angiogenesis / intracellular calcium ion homeostasis / G alpha (z) signalling events / calcium ion transport / histone binding / adaptive immune response / transcription coactivator activity / protein phosphorylation / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / signal transduction / extracellular exosome / zinc ion binding / 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. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / 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
Similarity search - Domain/homology
Chem-LY4 / Protein kinase C beta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.425 Å
AuthorsBriggs, D.C. / Parker, P.J. / McDonald, N.Q. / Brown, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2068 United Kingdom
CitationJournal: Biochem.J. / Year: 2025
Title: Penetrant PKCb mutation in ATLL displays a mixed gain-of-function.
Authors: Brown, S.J.L. / Briggs, D.C. / Costello, P. / Yaguchi, H. / Bangham, C.R.M. / Parker, P.J. / McDonald, N.Q.
History
DepositionAug 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform Beta-II of Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2202
Polymers40,7511
Non-polymers4691
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Elution peak by SEC is consistent with monomeric assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-9 kcal/mol
Surface area15550 Å2
Unit cell
Length a, b, c (Å)102.327, 102.327, 82.827
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Isoform Beta-II of Protein kinase C beta type / PKC-B / PKC-beta


Mass: 40751.324 Da / Num. of mol.: 1 / Mutation: D427N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCB, PKCB, PRKCB1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05771, protein kinase C
#2: Chemical ChemComp-LY4 / (9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE / LY333531


Mass: 468.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N4O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.17 / Details: 0.1M Citrate pH 5.17 12.3% PEG 6k / Temp details: Room Temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryocooled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.67 Å
DetectorType: DECTRIS EIGER2 XE CdTe 9M / Detector: PIXEL / Date: Aug 1, 2022
RadiationMonochromator: Double Crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67 Å / Relative weight: 1
ReflectionResolution: 3.42→60.511 Å / Num. obs: 7021 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.995 / Net I/σ(I): 3.8
Reflection shellResolution: 3.42→3.47 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 343 / CC1/2: 0.175

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
DIALS3.10.3-2-g650e29187-releasedata reduction
gemmi0.7.1data extraction
DIALSdata scaling
MrBUMPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.425→60.511 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 129.548 / SU ML: 0.79 / Cross valid method: FREE R-VALUE / ESU R Free: 0.628
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2897 364 5.196 %
Rwork0.2142 6642 -
all0.218 --
obs-7006 99.829 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 144.059 Å2
Baniso -1Baniso -2Baniso -3
1--0.507 Å2-0.253 Å2-0 Å2
2---0.507 Å20 Å2
3---1.644 Å2
Refinement stepCycle: LAST / Resolution: 3.425→60.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 35 0 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122633
X-RAY DIFFRACTIONr_bond_other_d0.0050.0162441
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.833563
X-RAY DIFFRACTIONr_angle_other_deg1.0591.7585649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.658518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65710449
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.00610122
X-RAY DIFFRACTIONr_chiral_restr0.1050.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023032
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02600
X-RAY DIFFRACTIONr_nbd_refined0.1920.2578
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1390.22400
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21243
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.246
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.210
X-RAY DIFFRACTIONr_nbd_other0.10.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0420.21
X-RAY DIFFRACTIONr_mcbond_it10.80910.7261258
X-RAY DIFFRACTIONr_mcbond_other10.810.7271258
X-RAY DIFFRACTIONr_mcangle_it16.52419.3961569
X-RAY DIFFRACTIONr_mcangle_other16.51919.3941570
X-RAY DIFFRACTIONr_scbond_it12.5411.7031375
X-RAY DIFFRACTIONr_scbond_other12.53511.7031376
X-RAY DIFFRACTIONr_scangle_it18.91321.21994
X-RAY DIFFRACTIONr_scangle_other18.90821.1991995
X-RAY DIFFRACTIONr_lrange_it23.781134.82810537
X-RAY DIFFRACTIONr_lrange_other23.78134.82610538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.425-3.5130.47280.3944610.3995000.7940.89197.80.396
3.513-3.6090.439310.3794740.3835050.8430.8781000.382
3.609-3.7140.423220.3634440.3664660.8240.8811000.368
3.714-3.8270.32270.3334560.3324830.8790.8961000.336
3.827-3.9520.338200.2854270.2874470.8980.9241000.286
3.952-4.0910.266240.2584250.2584490.9440.9441000.253
4.091-4.2440.278180.2154110.2184290.9560.9621000.203
4.244-4.4170.213220.193830.1914050.960.9711000.179
4.417-4.6120.203210.1533650.1553860.960.9821000.128
4.612-4.8360.286120.1653680.1693800.9550.981000.14
4.836-5.0950.258230.1873360.1923590.9490.9751000.153
5.095-5.4020.297140.1813430.1863570.9450.9771000.153
5.402-5.7720.355260.1992930.2123190.9370.9731000.168
5.772-6.2290.66870.1892890.1992960.8410.9761000.156
6.229-6.8170.307180.2172680.2232860.9290.9671000.181
6.817-7.6090.259120.1582440.1632560.9590.9811000.128
7.609-8.7630.278110.1452180.152290.9540.9851000.128
8.763-10.6770.194160.1511810.1551970.9750.9891000.142
10.677-14.870.22840.1651630.1671670.9980.9831000.154
14.87-60.5110.29880.421930.4121010.9330.8961000.372
Refinement TLS params.Method: refined / Origin x: -35.2416 Å / Origin y: 25.8061 Å / Origin z: 7.7793 Å
111213212223313233
T0.1318 Å2-0.0765 Å20.0086 Å2-0.0989 Å2-0.0401 Å2--0.0376 Å2
L4.5574 °21.1298 °20.3294 °2-3.5335 °2-0.8357 °2--3.069 °2
S-0.1811 Å °0.331 Å °-0.0884 Å °-0.4404 Å °0.2051 Å °0.1714 Å °0.1375 Å °-0.0086 Å °-0.024 Å °
Refinement TLS groupSelection: ALL

+
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