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- PDB-8se1: Structure of Full-length Human Protein Kinase C Beta 2 (PKCBII) i... -

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Basic information

Entry
Database: PDB / ID: 8se1
TitleStructure of Full-length Human Protein Kinase C Beta 2 (PKCBII) in the Inactive Conformation
ComponentsProtein kinase C beta type
KeywordsSIGNALING PROTEIN / Protein Kinase C Beta / kinase / phosphorylation / PKCb / PKC / kinase signalling / PRKCB
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 / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / negative regulation of D-glucose transmembrane transport / protein kinase C / 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 / calyx of Held / protein kinase C binding / VEGFR2 mediated cell proliferation / Activation of NF-kappaB in B cells / calcium channel regulator activity / B cell receptor signaling pathway / positive regulation of insulin secretion / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / G alpha (z) signalling events / 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 / cytosol / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein kinase C beta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsCong, A.T.Q. / Witter, T.L. / Bruinsma, E.S. / Jayaraman, S. / Dugan, M.B. / Hawse, J.R. / Goetz, M.P. / Schellenberg, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P50CA116201 United States
CitationJournal: To Be Published
Title: Molecular Basis of Allosteric Regulation and Pharmaceutical Targeting of Protein Kinase C b
Authors: Cong, A.T.Q. / Witter, T.L. / Bruinsma, E.S. / Bhattacharya, S.S. / Jayaraman, S. / Dugan, M.B. / Paluncic, J. / Kuffel, M.J. / Farmakes, J. / Alvey, J. / Wu, X. / Fields, A.P. / Pandey, A. ...Authors: Cong, A.T.Q. / Witter, T.L. / Bruinsma, E.S. / Bhattacharya, S.S. / Jayaraman, S. / Dugan, M.B. / Paluncic, J. / Kuffel, M.J. / Farmakes, J. / Alvey, J. / Wu, X. / Fields, A.P. / Pandey, A. / Hawse, J.R. / Goetz, M.P. / Schellenberg, M.J.
History
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C beta type
B: Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,67920
Polymers154,8662
Non-polymers1,81218
Water1,26170
1
A: Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,33910
Polymers77,4331
Non-polymers9069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,33910
Polymers77,4331
Non-polymers9069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.556, 89.098, 160.714
Angle α, β, γ (deg.)90.00, 107.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein kinase C beta type / PKC-B / PKC-beta


Mass: 77433.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCB, PKCB, PRKCB1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P05771, protein kinase C
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG8000, MES buffer, magnesium chloride / PH range: 5.0-6.0 / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. obs: 25781 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.906 / CC star: 0.975 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.352 / Χ2: 1.06 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allΧ2% possible allRrim(I) all
3.35-3.473.70.96226030.4640.7960.5821.11299.9
3.47-3.613.70.71925720.6140.8720.4341.06299.70.842
3.61-3.773.60.57925530.7180.9140.3531.03699.70.68
3.77-3.973.60.45225630.8090.9460.2761.08199.30.531
3.97-4.223.50.30825490.9060.9750.1911.06499.50.364
4.22-4.553.40.22425550.9450.9860.1421.019990.266
4.55-53.20.19125560.9430.9850.1271.05698.10.23
5-5.733.70.20825880.9540.9880.1251.05699.50.244
5.73-7.213.60.18126060.9620.990.1111.06299.80.213
7.21-503.40.0726360.9940.9980.0441.04498.40.083

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→48.75 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1287 4.99 %
Rwork0.199 --
obs0.2018 25776 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10081 0 78 70 10229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310403
X-RAY DIFFRACTIONf_angle_d0.60514047
X-RAY DIFFRACTIONf_dihedral_angle_d18.1633914
X-RAY DIFFRACTIONf_chiral_restr0.0441456
X-RAY DIFFRACTIONf_plane_restr0.0041810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.450.31951300.28582408X-RAY DIFFRACTION87
3.45-3.610.29411440.25812731X-RAY DIFFRACTION100
3.61-3.80.34531430.24012750X-RAY DIFFRACTION100
3.8-4.040.26221440.20932741X-RAY DIFFRACTION99
4.04-4.350.25611470.18162777X-RAY DIFFRACTION99
4.35-4.780.21491400.16652698X-RAY DIFFRACTION98
4.78-5.470.23791440.17182768X-RAY DIFFRACTION99
5.48-6.90.24481470.19112791X-RAY DIFFRACTION100
6.9-48.750.20331480.16682825X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7493-0.14850.81311.1315-0.43761.22670.27790.1774-0.4994-0.5883-0.16670.19140.63780.0017-0.05460.665-0.0129-0.06590.4495-0.12990.6305-6.39446.389733.0604
21.24890.64110.61940.54970.88231.69540.36650.5488-0.9637-0.0083-0.0275-0.10841.01610.0255-0.31010.8292-0.0328-0.10810.6924-0.33271.0734-9.7203-8.049620.7657
32.72780.47611.6780.18730.69652.49980.01350.4082-0.4304-0.0106-0.05480.14450.6197-0.01290.13740.5849-0.0634-0.03610.565-0.13540.8797-0.7745.018425.2779
41.8025-0.13280.21381.3566-0.30813.8210.1162-0.0791-0.36560.0331-0.1458-0.02060.3213-0.14080.01030.31160.0328-0.01080.34750.08240.418610.25712.754658.5532
51.25680.6887-0.66350.6505-0.38962.2789-0.18220.21420.1115-0.13810.10090.005-0.3397-0.19310.09060.5448-0.0683-0.05980.45770.05470.2988-5.072641.1791-22.4253
63.83091.66240.51143.7499-0.66453.741-0.1549-0.0414-0.17270.31220.1790.2607-0.2697-0.5938-0.02790.44230.0920.06110.40740.02220.2744-16.417134.65660.3119
70.84920.2442-0.26761.22140.10531.2081-0.03310.14590.2082-0.2401-0.3193-0.01710.303-0.62410.35090.47740.1406-0.00640.76370.01740.6286-12.988328.363227.3686
82.10980.54110.25171.40510.52583.0598-0.01-0.20910.2041-0.097-0.1050.2742-0.3488-0.20590.08210.36210.1266-0.02190.3387-0.09210.3781-5.951145.451448.9896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 353 )
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 670 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 146 )
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 298 )
7X-RAY DIFFRACTION7chain 'B' and (resid 299 through 353 )
8X-RAY DIFFRACTION8chain 'B' and (resid 354 through 670 )

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