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- PDB-7leo: C1B domain of Protein kinase C in complex with diacylglycerol-lac... -

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Basic information

Entry
Database: PDB / ID: 7leo
TitleC1B domain of Protein kinase C in complex with diacylglycerol-lactone (AJH-836) and 1,2-diheptanoyl-sn-glycero-3-phosphocholine
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 / ATP binding / nucleus / metal ion binding / plasma membrane
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, 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 / Chem-XZJ / Protein kinase C delta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKatti, S.S. / Krieger, I.
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 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,28610
Polymers12,1942
Non-polymers2,0928
Water1,09961
1
A: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6766
Polymers6,0971
Non-polymers1,5795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6114
Polymers6,0971
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.388, 50.888, 37.485
Angle α, β, γ (deg.)90.000, 107.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-304-

XP5

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Components

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


Mass: 6097.217 Da / Num. of mol.: 2 / 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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: 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.: 3 / Source method: obtained synthetically / Formula: C22H45NO8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XZJ / {(2R,4E)-2-(hydroxymethyl)-4-[5-methyl-3-(2-methylpropyl)hexylidene]-5-oxooxolan-2-yl}methyl 2,2-dimethylpropanoate / AJH-836


Mass: 382.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
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 condition: Protein 2 mM in MES pH 6.5, 150 mM KCl; Phosphatidylcholine: 20 mM; AJH-836: 2.2 mM

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 17721 / % possible obs: 98.5 % / Redundancy: 5.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.049 / Rrim(I) all: 0.116 / Χ2: 2.096 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.683.70.8318820.5680.4790.9640.6198.1
1.68-1.714.10.8338660.6410.4560.9530.60199.1
1.71-1.744.50.7468950.7960.3910.8460.70598.8
1.74-1.784.90.6388810.830.3210.7170.72798.8
1.78-1.8250.6428810.8040.3180.7190.78298.5
1.82-1.864.90.5738680.8670.2870.6440.83597.1
1.86-1.95.70.668700.8510.3070.730.95497.5
1.9-1.965.80.4849010.9050.2180.5321.57899.2
1.96-2.015.90.378640.940.1690.4081.15598.9
2.01-2.085.90.2968960.9510.1340.3261.499.4
2.08-2.155.90.2588920.9570.1150.2841.6198.9
2.15-2.245.40.2168730.9720.1020.242.02697.1
2.24-2.3460.2018940.9770.0910.2212.50198.9
2.34-2.466.10.1588770.9890.0710.1732.17798.5
2.46-2.6260.1389030.9850.0620.1512.73299.6
2.62-2.825.80.1228820.9850.0570.1353.23498.5
2.82-3.115.70.1048980.9910.0480.1153.41998.2
3.11-3.555.90.0918900.9910.0420.1498.7
3.55-4.485.20.0758880.9940.0350.0834.25697.3
4.48-505.40.0769200.9920.0370.0854.53198

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ptq

1ptq


Resolution: 1.65→29.96 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 908 5.13 %
Rwork0.2237 16789 -
obs0.2248 17697 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.03 Å2 / Biso mean: 36.7592 Å2 / Biso min: 20.41 Å2
Refinement stepCycle: final / Resolution: 1.65→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 159 61 1039
Biso mean--43.61 41.11 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006991
X-RAY DIFFRACTIONf_angle_d1.11321
X-RAY DIFFRACTIONf_dihedral_angle_d45.241191
X-RAY DIFFRACTIONf_chiral_restr0.096123
X-RAY DIFFRACTIONf_plane_restr0.005154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.740.31721250.26052442256784
1.74-1.880.32131550.24872837299298
1.88-2.070.29651360.25142864300099
2.07-2.360.25711640.23862859302398
2.36-2.980.2361700.2482870304099
2.98-29.960.22581580.20242917307598

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