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- PDB-6iej: The C2 domain of cytosolic phospholipase A2 alpha bound to phosph... -

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Basic information

Entry
Database: PDB / ID: 6iej
TitleThe C2 domain of cytosolic phospholipase A2 alpha bound to phosphatidylcholine
ComponentsCytosolic phospholipase A2
KeywordsHYDROLASE / Lipid binding / Phospholipase / Calcium binding / C2 domain
Function / homology
Function and homology information


phospho-PLA2 pathway / Acyl chain remodeling of CL / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Hydrolysis of LPC / Synthesis of PA / Arachidonic acid metabolism / Platelet sensitization by LDL / Acyl chain remodelling of PC / Acyl chain remodelling of PS ...phospho-PLA2 pathway / Acyl chain remodeling of CL / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Hydrolysis of LPC / Synthesis of PA / Arachidonic acid metabolism / Platelet sensitization by LDL / Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / glycerophospholipid catabolic process / COPI-independent Golgi-to-ER retrograde traffic / phosphatidyl phospholipase B activity / lysophospholipase / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / calcium-dependent phospholipase A2 activity / lysophospholipase activity / ADP signalling through P2Y purinoceptor 1 / calcium-dependent phospholipid binding / phospholipase A2 / phospholipase A2 activity / cytoplasmic vesicle / calcium ion binding / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol
Similarity search - Function
Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / C2 domain / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / C2 domain / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,2-dihexanoyl-sn-glycero-3-phosphocholine / Cytosolic phospholipase A2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å
AuthorsHirano, Y. / Gao, Y.G. / Stephenson, D.J. / Vu, N.T. / Malinina, L. / Chalfant, C.E. / Patel, D.J. / Brown, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL125353 United States
CitationJournal: Elife / Year: 2019
Title: Structural basis of phosphatidylcholine recognition by the C2-domain of cytosolic phospholipase A2alpha.
Authors: Hirano, Y. / Gao, Y.G. / Stephenson, D.J. / Vu, N.T. / Malinina, L. / Simanshu, D.K. / Chalfant, C.E. / Patel, D.J. / Brown, R.E.
History
DepositionSep 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 22, 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: Cytosolic phospholipase A2
B: Cytosolic phospholipase A2
C: Cytosolic phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69117
Polymers42,9183
Non-polymers1,77314
Water1,47782
1
A: Cytosolic phospholipase A2
B: Cytosolic phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,78611
Polymers28,6122
Non-polymers1,1749
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-88 kcal/mol
Surface area13100 Å2
MethodPISA
2
C: Cytosolic phospholipase A2
hetero molecules

C: Cytosolic phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,81012
Polymers28,6122
Non-polymers1,19810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area1490 Å2
ΔGint-91 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.294, 187.388, 68.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11C-204-

MG

21B-328-

HOH

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Components

#1: Protein Cytosolic phospholipase A2 / Cytosolic phospholipase A2 alpha / cPLA2 / Phospholipase A2 group IVA


Mass: 14306.147 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: PLA2G4A, CPLA2, PLA2G4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star (DE3) / References: UniProt: P49147, phospholipase A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HXG / 1,2-dihexanoyl-sn-glycero-3-phosphocholine / (4R,7R)-7-(hexanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphapentadecan-1-aminium 4-oxide


Mass: 454.515 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H41NO8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 4.08 Å3/Da / Density % sol: 69.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 100 mM HEPES-NaOH buffer, 1.4 M magnesium chloride, 0.6 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35668 / % possible obs: 99.5 % / Redundancy: 7.7 % / Rsym value: 0.059 / Net I/σ(I): 30.9
Reflection shellResolution: 2.2→2.24 Å / Rsym value: 0.363

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RLW

1rlw


Resolution: 2.206→46.881 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1816 5.16 %
Rwork0.2244 --
obs0.2256 35185 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.206→46.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 86 82 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083131
X-RAY DIFFRACTIONf_angle_d1.1174267
X-RAY DIFFRACTIONf_dihedral_angle_d18.6231170
X-RAY DIFFRACTIONf_chiral_restr0.054499
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2062-2.26590.38711000.27812237X-RAY DIFFRACTION88
2.2659-2.33260.26211390.27182523X-RAY DIFFRACTION98
2.3326-2.40790.271630.24522556X-RAY DIFFRACTION100
2.4079-2.49390.31631270.24482565X-RAY DIFFRACTION100
2.4939-2.59380.33091220.2392585X-RAY DIFFRACTION100
2.5938-2.71180.27411320.25962586X-RAY DIFFRACTION100
2.7118-2.85470.30261670.28422567X-RAY DIFFRACTION100
2.8547-3.03360.31331440.27762563X-RAY DIFFRACTION100
3.0336-3.26770.28941620.25182570X-RAY DIFFRACTION100
3.2677-3.59650.19081500.21282598X-RAY DIFFRACTION100
3.5965-4.11660.24311520.20022589X-RAY DIFFRACTION100
4.1166-5.18550.21021400.17422658X-RAY DIFFRACTION100
5.1855-46.89180.23571180.23372772X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -43.3847 Å / Origin y: -17.8458 Å / Origin z: 17.7473 Å
111213212223313233
T0.3488 Å20.1112 Å20.0764 Å2-0.3362 Å2-0.0069 Å2--0.5032 Å2
L0.7317 °20.0951 °20.2376 °2-0.5752 °2-0.0564 °2--1.0803 °2
S-0.1155 Å °-0.0121 Å °-0.0198 Å °-0.0462 Å °-0.0197 Å °-0.0163 Å °0.2954 Å °0.1975 Å °0.1277 Å °
Refinement TLS groupSelection details: all

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