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- PDB-8se3: Structure of Full-length Human Protein Kinase C Beta 1 (PKCBI) in... -

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Basic information

Entry
Database: PDB / ID: 8se3
TitleStructure of Full-length Human Protein Kinase C Beta 1 (PKCBI) in the Active Conformation
ComponentsProtein kinase C beta type
KeywordsSIGNALING PROTEIN / TRANSFERASE / 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
Protein kinase C beta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCong, A.T.Q. / Witter, T.L. / Bruinsma, E.S. / Jayaraman, S. / Hawse, J.R. / Goetz, M.P. / Schellenberg, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA233700 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9199
Polymers77,2891
Non-polymers6308
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.198, 163.158, 77.319
Angle α, β, γ (deg.)90.00, 100.41, 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: 77288.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCB, PKCB, PRKCB1 / Cell line (production host): H293F / Production host: Homo sapiens (human) / References: UniProt: P05771, protein kinase C
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, sodium citrate / PH range: 7.0-8.0 / 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: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 10, 2020
RadiationMonochromator: 0.97911 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 30360 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Rrim(I) all: 0.161 / Χ2: 1.022 / Net I/σ(I): 6.5 / Num. measured all: 210297
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allΧ2% possible allRrim(I) all
2.6-2.697.11.48530320.4860.8090.5950.99899.7
2.69-2.871.12930120.630.8790.456199.71.219
2.8-2.936.90.85930480.7680.9320.351.01199.60.929
2.93-3.086.50.55430180.8780.9670.2341.00899.30.603
3.08-3.286.80.36830200.9420.9850.1511.04799.20.398
3.28-3.537.30.22630360.980.9950.0891.08699.70.244
3.53-3.887.10.14730390.9890.9970.0591.04299.70.159
3.88-4.456.70.09330240.9940.9990.0390.98599.20.101
4.45-5.670.07130430.9960.9990.0290.99399.20.077
5.6-506.90.08430880.9930.9980.0341.04899.40.091

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.66 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1520 5.01 %
Rwork0.1971 --
obs0.1986 30355 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4871 0 28 71 4970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025018
X-RAY DIFFRACTIONf_angle_d0.5196766
X-RAY DIFFRACTIONf_dihedral_angle_d17.8371885
X-RAY DIFFRACTIONf_chiral_restr0.043704
X-RAY DIFFRACTIONf_plane_restr0.003871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.34721380.33372539X-RAY DIFFRACTION97
2.69-2.780.31431390.31992627X-RAY DIFFRACTION100
2.78-2.90.35381380.29782612X-RAY DIFFRACTION100
2.9-3.030.31811350.29332625X-RAY DIFFRACTION99
3.03-3.190.29381430.25932619X-RAY DIFFRACTION99
3.19-3.390.23971340.22632620X-RAY DIFFRACTION100
3.39-3.650.25091440.19752627X-RAY DIFFRACTION100
3.65-4.010.21021280.1742636X-RAY DIFFRACTION100
4.02-4.60.19421440.14982640X-RAY DIFFRACTION99
4.6-5.790.17891400.15312620X-RAY DIFFRACTION100
5.79-48.660.18991370.17432670X-RAY DIFFRACTION99
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)
10.762-1.14990.49722.7599-1.50230.87190.06860.2041-0.22050.81020.31690.8651-0.7847-0.715-0.08371.33620.64880.13541.3018-0.05360.577423.8516-20.60128.9106
21.3619-0.3810.49433.15921.58482.00330.253-0.07620.03340.1237-0.04530.26990.3199-0.1998-0.31820.49580.0173-0.02110.5499-0.02030.624334.229-48.337219.4553
33.16270.751.4768.99753.13724.9866-0.0569-0.37880.43680.27360.1725-0.7044-1.16330.17790.09880.77520.1014-0.04270.463-0.08520.609243.5147-28.094620.4486
42.6550.32320.44421.4077-0.18121.5581-0.3882-0.01620.2845-0.14920.0823-0.54260.00380.35290.22260.44810.051-0.06770.4764-0.00130.703114.401719.95020.633
52.2424-0.00890.48063.3375-0.26062.52650.07740.16960.26170.0569-0.4984-0.1699-0.75430.1450.47560.4933-0.0036-0.03590.50280.01860.68513.313221.5661.2957
61.6071-0.5659-1.09120.42290.17711.633-0.00460.1462-0.1794-0.369-0.1558-0.19680.2087-0.07040.05970.64830.2265-0.00590.64610.01260.701322.248111.0085-1.8065
70.6378-0.63430.49792.7427-0.04231.85920.20020.6117-0.5174-0.1441-0.24790.15370.76740.64440.05930.95280.2368-0.08910.6936-0.0950.659310.94231.3866-7.119
82.5193-1.01780.1541.78030.76311.0623-0.07250.2995-0.512-0.48960.1375-0.21670.53770.4263-0.0980.78940.1025-0.04360.5019-0.03570.648411.65555.2964-5.7208
91.71110.42070.67361.2602-0.90021.2367-0.8341-1.20180.45611.33170.58690.00250.59830.6384-0.06171.32720.7813-0.06881.2455-0.13720.441514.87447.642229.3663
101.0711.05841.62068.08091.51152.4866-0.5855-1.1245-0.41450.73410.29741.51341.02320.13260.01771.28440.60220.25920.87310.11130.64554.76437.082928.1407
110.2836-0.12050.0221.6402-0.78340.7706-0.5916-1.06620.01770.70670.7186-0.23980.56040.5818-0.04841.26160.9336-0.21411.1882-0.03080.618720.91533.681624.1155
124.688-2.4109-0.5413.18861.01655.2427-1.1261-0.1786-0.09580.66480.48190.37841.34120.23120.4031.07350.47620.02180.84260.01520.51716.27121.766118.1048
131.0896-0.39910.9763.925-0.52621.15350.2920.1196-0.36610.7133-0.15570.00540.236-0.01290.14530.48080.11250.01250.6136-0.06350.42436.0482-34.772126.8808
141.678-0.7576-0.58373.2082.2124.93480.4330.1587-0.5346-0.4412-0.08270.3285-0.2842-0.5842-0.24820.45570.1203-0.07290.3935-0.02760.512635.3606-43.450216.555
151.27650.36130.74463.2309-1.35023.43710.08760.1024-0.0135-0.11940.1452-0.10340.0828-0.2732-0.28830.47950.08850.02650.4272-0.00360.377137.2222-33.38315.8247
161.9749-1.14130.61142.8617-0.13252.10330.2086-0.5471-0.14890.6678-0.17931.16970.3889-1.12840.09040.8920.29790.33811.37310.25411.050812.0698-22.597819.6752
171.9474-0.1891-0.53970.72290.43551.5689-0.4041-0.5122-0.23660.69590.52260.2557-0.3814-0.2828-0.05450.64950.2970.13860.59180.1540.513925.7357-20.916912.2885
181.3585-0.21640.0282.15041.59514.11080.055-0.0661-0.2537-0.26420.27690.469-0.1833-0.3365-0.25960.41340.0910.01840.62210.06220.575132.4286-28.81881.8911
192.1277-1.58150.63813.08950.55662.7228-0.18210.0787-0.3551-0.12090.23231.0013-0.3772-0.4983-0.03410.44970.20080.03590.63080.1580.762617.2734-20.80551.9209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 611 through 629 )
2X-RAY DIFFRACTION2chain 'A' and (resid 630 through 657 )
3X-RAY DIFFRACTION3chain 'A' and (resid 658 through 671 )
4X-RAY DIFFRACTION4chain 'A' and (resid 30 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 116 )
8X-RAY DIFFRACTION8chain 'A' and (resid 117 through 155 )
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 238 )
10X-RAY DIFFRACTION10chain 'A' and (resid 239 through 253 )
11X-RAY DIFFRACTION11chain 'A' and (resid 254 through 276 )
12X-RAY DIFFRACTION12chain 'A' and (resid 277 through 292 )
13X-RAY DIFFRACTION13chain 'A' and (resid 293 through 366 )
14X-RAY DIFFRACTION14chain 'A' and (resid 367 through 381 )
15X-RAY DIFFRACTION15chain 'A' and (resid 382 through 427 )
16X-RAY DIFFRACTION16chain 'A' and (resid 428 through 439 )
17X-RAY DIFFRACTION17chain 'A' and (resid 440 through 480 )
18X-RAY DIFFRACTION18chain 'A' and (resid 481 through 499 )
19X-RAY DIFFRACTION19chain 'A' and (resid 501 through 610 )

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