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- PDB-7lcb: C1B domain of Protein kinase C in complex with prostratin and pho... -

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Basic information

Entry
Database: PDB / ID: 7lcb
TitleC1B domain of Protein kinase C in complex with prostratin and phosphatidylcholine
ComponentsProtein kinase C delta type
KeywordsLIPID BINDING PROTEIN / C1 / lipid-binding / diacylglycerol-binding / Zn2+ finger
Function / homology
Function and homology information


protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / zinc ion binding / ATP binding / nucleus
Similarity search - Function
Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta 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. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta 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. / 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-XP5 / prostratin / Protein kinase C delta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKatti, S.S. / Krieger, I.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108998 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists.
Authors: Katti, S.S. / Krieger, I.V. / Ann, J. / Lee, J. / Sacchettini, J.C. / Igumenova, T.I.
History
DepositionJan 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1015
Polymers6,0971
Non-polymers1,0044
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4400 Å2
Unit cell
Length a, b, c (Å)34.402, 25.869, 57.964
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein Protein kinase C delta type / nPKC-delta


Mass: 6097.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkcd, rCG_42255 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140UHX0, protein kinase C
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-XYV / prostratin / 12-deoxyphorbol-13-acetate / (1aR,1bS,4aR,7aS,7bR,8R,9aS)-4a,7b-dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1,1a,1b,4,4a,5,7a,7b,8,9-decahydro-9aH-cyclopropa[3,4]benzo[1,2-e]azulen-9a-yl acetate


Mass: 390.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XP5 / (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide


Mass: 482.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H45NO8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Screen condition: 0.2 M Ammonium acetate 0.1 M Sodium Phosphate 30% Isopropanol pH 6.8; Drop condition: Protein: 2 mM in MES pH 6.5, 150 mM KCl; Phosphatidylcholine: 20 mM; Prostratin: 2.5 mM

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→44.6 Å / Num. obs: 5115 / % possible obs: 89.1 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.0558 / Net I/σ(I): 15.48
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.2636 / Mean I/σ(I) obs: 3 / Num. unique obs: 441 / % possible all: 48.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SAINTdata reduction
SAINTdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ptq

1ptq


Resolution: 1.7→28.75 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 243 4.75 %
Rwork0.1719 4870 -
obs0.174 5113 89.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.92 Å2 / Biso mean: 17.4806 Å2 / Biso min: 4.92 Å2
Refinement stepCycle: final / Resolution: 1.7→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms417 0 62 38 517
Biso mean--28.81 23.07 -
Num. residues----52
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009506
X-RAY DIFFRACTIONf_angle_d1.445690
X-RAY DIFFRACTIONf_dihedral_angle_d44.53985
X-RAY DIFFRACTIONf_chiral_restr0.08968
X-RAY DIFFRACTIONf_plane_restr0.00780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-2.140.29351010.19552134223578
2.14-28.750.18851420.163427362878100

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