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- PDB-9c5f: Crystal Structure Analysis of human PRKCB -

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Basic information

Entry
Database: PDB / ID: 9c5f
TitleCrystal Structure Analysis of human PRKCB
ComponentsProtein kinase C beta type
KeywordsTRANSFERASE / KINASE / Calcium-phytate / B-cell activation / apoptosis
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 / nuclear androgen receptor binding / lipoprotein transport / 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 / 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: 2.41 Å
AuthorsSeo, H.-S. / Oh, B.-C. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of PARP1 in complex with a compound
Authors: Seo, H.-S. / Dhe-Paganon, S. / Arthanari, H.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: 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)45,93024
Polymers44,1522
Non-polymers1,77722
Water30617
1
A: Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,86911
Polymers22,0761
Non-polymers79310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase C beta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,06113
Polymers22,0761
Non-polymers98512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.123, 144.123, 70.369
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 22076.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCB, PKCB, PRKCB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05771, protein kinase C
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Ammonium sulfate, 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.41→61.3 Å / Num. obs: 32787 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1016 / Rpim(I) all: 0.03347 / Rrim(I) all: 0.107 / Net I/σ(I): 11.09
Reflection shellResolution: 2.41→2.48 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 2664 / CC1/2: 0.406

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→61.3 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1627 4.99 %
Rwork0.2133 --
obs0.2142 32608 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→61.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 86 17 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032374
X-RAY DIFFRACTIONf_angle_d0.6453226
X-RAY DIFFRACTIONf_dihedral_angle_d21.832864
X-RAY DIFFRACTIONf_chiral_restr0.046342
X-RAY DIFFRACTIONf_plane_restr0.008405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.480.34431180.35772519X-RAY DIFFRACTION97
2.48-2.560.32641700.33762482X-RAY DIFFRACTION98
2.56-2.650.39211520.39992528X-RAY DIFFRACTION99
2.65-2.760.40891620.34722527X-RAY DIFFRACTION99
2.76-2.880.3771970.3162616X-RAY DIFFRACTION100
2.88-3.030.33671250.28712560X-RAY DIFFRACTION100
3.03-3.220.30791180.27352605X-RAY DIFFRACTION100
3.22-3.470.31281260.24042600X-RAY DIFFRACTION100
3.47-3.820.2061170.21612612X-RAY DIFFRACTION100
3.82-4.380.18011520.17232603X-RAY DIFFRACTION100
4.38-5.510.19121320.16032633X-RAY DIFFRACTION100
5.51-61.30.18451580.17892696X-RAY DIFFRACTION100
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)
10.1293-0.1003-0.15810.18840.08580.9653-0.05320.8035-0.9705-0.3262-1.28330.39342.6915-0.65440.0051.0912-0.0450.27021.2097-0.12841.2711-19.071448.6674-5.1422
22.20870.117-0.5962.2381-0.32322.50850.1471-1.233-0.0160.3814-0.3588-0.16330.19210.3915-0.00050.4953-0.16240.02360.8097-0.10510.5348-22.878359.11297.5311
30.91251.2658-0.02741.81390.1630.4323-0.59480.2122.3864-1.36880.23691.7609-1.9805-1.81250.02160.97930.00620.02551.1021-0.17661.2059-38.150864.33314.5118
45.82962.1501-2.01142.9284-1.25915.74270.1424-0.78230.06780.1155-0.29180.21660.3779-0.09030.00160.5891-0.17050.03150.7491-0.1230.6182-27.012857.20895.4211
50.047-0.03940.00080.02330.01090.0029-0.3769-1.64710.60690.69490.4407-1.3372-0.78162.07580.00851.0027-0.1683-0.02071.30890.0951.0848-3.434763.6131-2.9295
60.20520.23710.16980.23410.19720.1447-0.4824-1.093-1.66420.0738-0.0864-0.42060.94611.4676-0.00990.83160.10370.39991.02280.02341.18564.904854.9399-18.6959
70.10820.1370.10720.15390.13230.1068-1.20550.3046-1.16-1.28360.3429-1.50911.46291.43620.00210.71970.01280.35911.2497-0.03331.17247.433758.7273-27.9301
81.08070.0701-0.330.9284-0.26581.5596-0.77060.5481-0.9638-0.54220.1952-0.3620.9154-0.00720.0020.7119-0.1130.07920.7495-0.07360.6871-10.317957.4176-15.9175
92.35641.870.27022.29440.89350.5882-0.21931.01962.091-1.88290.23282.1093-0.8606-1.060.01560.816-0.1783-0.0581.17830.07320.9444-3.396870.3435-27.9806
102.43121.2131-1.84050.6415-0.60863.3166-1.41151.0075-1.7239-0.49590.49320.10061.62890.1493-0.21971.1575-0.29370.30640.7802-0.29691.0409-10.190451.1325-19.6712
110.7379-0.37510.30740.2032-0.15630.1525-0.19580.87840.63060.0382-0.62970.23030.1699-0.6917-0.05770.7146-0.12360.16411.15590.00290.86436.292766.9316-28.173
120.1037-0.1877-0.06630.9402-0.96511.845-0.69110.6880.1205-0.35710.3986-0.0387-0.0397-0.6725-0.00620.4751-0.14550.03080.87330.00840.6043-12.363.4903-18.8066
130.4864-0.31270.11211.5488-0.11961.4391-0.3055-0.1978-0.2766-0.2301-0.1799-0.47440.14250.7804-0.01170.5863-0.03480.06621.06140.09220.83023.556164.187-17.1619
141.83861.0357-0.06831.0155-1.07632.25010.1352-0.7453-0.3119-0.252-0.4833-0.74320.14321.1840.00320.53120.0370.06990.8480.13370.81031.769861.5769-12.398
150.2352-0.0021-0.03790.29830.20940.6729-0.2489-0.4054-0.18810.82210.07210.3655-0.09411.0252-0.0010.9211-0.04680.07361.49010.10661.04145.018962.4661-9.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 150 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 201 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 291 )
5X-RAY DIFFRACTION5chain 'B' and (resid 150 through 160 )
6X-RAY DIFFRACTION6chain 'B' and (resid 161 through 168 )
7X-RAY DIFFRACTION7chain 'B' and (resid 169 through 177 )
8X-RAY DIFFRACTION8chain 'B' and (resid 178 through 201 )
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 211 )
10X-RAY DIFFRACTION10chain 'B' and (resid 212 through 224 )
11X-RAY DIFFRACTION11chain 'B' and (resid 225 through 238 )
12X-RAY DIFFRACTION12chain 'B' and (resid 239 through 253 )
13X-RAY DIFFRACTION13chain 'B' and (resid 254 through 268 )
14X-RAY DIFFRACTION14chain 'B' and (resid 269 through 284 )
15X-RAY DIFFRACTION15chain 'B' and (resid 285 through 291 )

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