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- PDB-7l92: C1B domain of Protein kinase C in complex with diacylglycerol and... -

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Basic information

Entry
Database: PDB / ID: 7l92
TitleC1B domain of Protein kinase C in complex with diacylglycerol and dodecyl 2-(trimethylammonio)ethyl phosphate
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
DIACYL GLYCEROL / dodecyl 2-(trimethylammonio)ethyl phosphate / ETHANOL / Protein kinase C delta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1, 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
D: Protein kinase C delta type
G: Protein kinase C delta type
J: Protein kinase C delta type
M: Protein kinase C delta type
P: Protein kinase C delta type
S: Protein kinase C delta type
V: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,27542
Polymers48,7788
Non-polymers9,49834
Water4,161231
1
A: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5246
Polymers6,0971
Non-polymers1,4275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2055
Polymers6,0971
Non-polymers1,1074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4785
Polymers6,0971
Non-polymers1,3814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2055
Polymers6,0971
Non-polymers1,1074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2055
Polymers6,0971
Non-polymers1,1074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2055
Polymers6,0971
Non-polymers1,1074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2516
Polymers6,0971
Non-polymers1,1535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
V: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2055
Polymers6,0971
Non-polymers1,1074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.068, 89.068, 218.679
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11M-437-

HOH

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Components

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Protein , 1 types, 8 molecules ADGJMPSV

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


Mass: 6097.217 Da / Num. of mol.: 8 / Fragment: C1B domain
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

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Non-polymers , 5 types, 265 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C39H76O5
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical
ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H38NO4P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.42 Å3/Da / Density % sol: 64.06 %
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 15% Isopropanol pH 6.8 Drop conditions: For seed crystals Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 20 mM ...Details: Screen condition: 0.2 M Ammonium acetate 0.1 M Sodium phosphate 15% Isopropanol pH 6.8 Drop conditions: For seed crystals Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 20 mM 1,2-dioctanoyl-sn-glycerol: 2.5 mM Final drop Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 10 mM 1,2-dioctanoyl-sn-glycerol: 2.5 mM

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.75→44.6 Å / Num. obs: 64618 / % possible obs: 99.1 % / Redundancy: 2.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.613 / Num. unique obs: 3574 / CC1/2: 0.528

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Processing

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

1ptq


Resolution: 1.75→28.96 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 3397 5.26 %
Rwork0.2142 61202 -
obs0.216 64599 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.24 Å2 / Biso mean: 40.2307 Å2 / Biso min: 14.23 Å2
Refinement stepCycle: final / Resolution: 1.75→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 447 231 3997
Biso mean--53.08 39.89 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.780.35771460.339425592705100
1.78-1.80.36781130.331825292642100
1.8-1.830.34721220.32226052727100
1.83-1.860.34361450.2926112756100
1.86-1.890.33361630.296425232686100
1.89-1.930.36621660.303325132679100
1.93-1.960.35061280.276625892717100
1.96-20.33011300.28226112741100
2-2.050.3321200.281925522672100
2.05-2.090.34721270.285126052732100
2.09-2.150.30531820.268525572739100
2.15-2.20.3352820.251626552737100
2.2-2.270.25891590.23125222681100
2.27-2.340.30741730.245525712744100
2.34-2.430.24331440.251725332677100
2.43-2.520.30521300.23732557268799
2.52-2.640.30281520.23652531268399
2.64-2.780.28281380.22472554269299
2.78-2.950.30661380.22882547268599
2.95-3.180.26841270.22272541266898
3.18-3.50.21151190.1912530264997
3.5-40.18131480.1712499264797
4-5.040.18651760.15212474265097
5.04-28.960.20621690.182434260395

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