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- PDB-4x95: Crystal structure of fully glycosylated Lysosomal Phospholipase A... -

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Basic information

Entry
Database: PDB / ID: 4x95
TitleCrystal structure of fully glycosylated Lysosomal Phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (MAFP)
ComponentsGroup XV phospholipase A2
KeywordsTRANSFERASE / hydrolase / phospholipase / MAFP / acyltransferase
Function / homology
Function and homology information


acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity ...acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / calcium-independent phospholipase A2 activity / diacylglycerol biosynthetic process / phosphatidylglycerol metabolic process / ceramide metabolic process / phosphatidylcholine catabolic process / fatty acid catabolic process / phosphatidylcholine metabolic process / lysophospholipase activity / phospholipase A2 / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phospholipid binding / lysosome / intracellular membrane-bounded organelle / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane
Similarity search - Function
Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYL ARACHIDONYL FLUOROPHOSPHONATE / Lysosomal phospholipase A and acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsGlukhova, A. / Tesmer, J.J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase.
Authors: Glukhova, A. / Hinkovska-Galcheva, V. / Kelly, R. / Abe, A. / Shayman, J.A. / Tesmer, J.J.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group XV phospholipase A2
B: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,48312
Polymers86,2422
Non-polymers3,24110
Water00
1
A: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7426
Polymers43,1211
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7426
Polymers43,1211
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.385, 125.275, 140.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 377 / Label seq-ID: 5 - 378

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Group XV phospholipase A2 / 1-O-acylceramide synthase / ACS / LCAT-like lysophospholipase / LLPL / Lysophospholipase 3 / ...1-O-acylceramide synthase / ACS / LCAT-like lysophospholipase / LLPL / Lysophospholipase 3 / Lysosomal phospholipase A2 / LPLA2


Mass: 43121.027 Da / Num. of mol.: 2 / Fragment: UNP residues 34-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G15, LYPLA3, UNQ341/PRO540 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q8NCC3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MAY / METHYL ARACHIDONYL FLUOROPHOSPHONATE / MAFP


Mass: 370.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36FO2P / Comment: inhibitor*YM

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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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 100 mM Na citrate pH 3.5-4, 20% PEG 3350, and 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.08→30 Å / Num. obs: 12079 / % possible obs: 49.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.076 / Rrim(I) all: 0.19 / Χ2: 1.265 / Net I/av σ(I): 11.1 / Net I/σ(I): 4.2 / Num. measured all: 61572
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.152.60.342540.7830.2440.4230.2154.5
3.15-3.2140.4631120.8270.2520.5320.2559.3
3.21-3.274.60.3671860.8750.1770.4090.35415.7
3.27-3.345.10.3782360.8360.1750.4190.44119.7
3.34-3.415.40.3922950.8690.1770.4320.38124.9
3.41-3.495.60.363450.8730.1570.3940.60528.3
3.49-3.585.80.3463690.9270.1490.3780.64230.9
3.58-3.675.90.3394180.950.1430.3690.70534.3
3.67-3.785.90.3224690.9090.1370.3510.83539.5
3.78-3.95.90.3025080.9420.1290.331.10641.3
3.9-4.045.80.2845650.9650.1220.311.20846.8
4.04-4.215.80.2895940.9640.1230.3151.45249.6
4.21-4.45.60.2396810.9680.1040.2621.39255.5
4.4-4.635.40.2087260.9870.090.2271.43859.3
4.63-4.925.10.2028280.9830.0890.2221.56467.9
4.92-5.2950.199000.9880.0830.2081.3773.1
5.29-5.824.70.18610490.9820.0810.2031.41785.3
5.82-6.664.60.15811740.9870.0690.1731.24693
6.66-8.364.60.11912510.9910.0530.1311.49499.3
8.36-304.40.07413190.9940.0350.0822.02698.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X90

4x90


Resolution: 3.08→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 54.643 / SU ML: 0.407 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.736 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 615 5.1 %RANDOM
Rwork0.2177 ---
obs0.2195 11420 49.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 256.14 Å2 / Biso mean: 150.015 Å2 / Biso min: 103.97 Å2
Baniso -1Baniso -2Baniso -3
1-42.72 Å20 Å20 Å2
2---17.63 Å20 Å2
3----25.09 Å2
Refinement stepCycle: final / Resolution: 3.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 176 0 6217
Biso mean--199.47 --
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196408
X-RAY DIFFRACTIONr_bond_other_d0.0020.025943
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9918750
X-RAY DIFFRACTIONr_angle_other_deg0.746313635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9985750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96723.495289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1821541
X-RAY DIFFRACTIONr_chiral_restr0.0730.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021491
X-RAY DIFFRACTIONr_mcbond_it2.62710.6083006
X-RAY DIFFRACTIONr_mcbond_other2.62610.6073005
X-RAY DIFFRACTIONr_mcangle_it4.45515.9043754
Refine LS restraints NCS

Ens-ID: 1 / Number: 23133 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.08→3.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 3 -
Rwork0.362 80 -
all-83 -
obs--4.71 %
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)
11.0226-0.3623-0.70273.01180.44182.09590.0103-0.109-0.04730.1205-0.07580.0598-0.0095-0.03070.06550.0181-0.0128-0.06770.1909-0.0040.39183.1678.800122.5619
21.5017-0.43840.11832.359-0.3612.5926-0.02050.13190.1752-0.0073-0.0516-0.7063-0.47370.50980.0720.13-0.2198-0.01560.49030.08230.960925.435931.3639-6.6904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 386
2X-RAY DIFFRACTION2B3 - 386

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