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- PDB-8pc4: MEMBRANE TARGET COMPLEX 1 -

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Basic information

Entry
Database: PDB / ID: 8pc4
TitleMEMBRANE TARGET COMPLEX 1
ComponentsN-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
KeywordsMEMBRANE PROTEIN / Membrane / Target / Dimer / Drug
Function / homology
Function and homology information


N-acetylphosphatidylethanolamine-hydrolysing phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / Biosynthesis of A2E, implicated in retinal degradation / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / smooth endoplasmic reticulum membrane / host-mediated regulation of intestinal microbiota composition / phospholipid catabolic process / bile acid binding / photoreceptor outer segment membrane ...N-acetylphosphatidylethanolamine-hydrolysing phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / Biosynthesis of A2E, implicated in retinal degradation / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / smooth endoplasmic reticulum membrane / host-mediated regulation of intestinal microbiota composition / phospholipid catabolic process / bile acid binding / photoreceptor outer segment membrane / temperature homeostasis / positive regulation of brown fat cell differentiation / hippocampal mossy fiber to CA3 synapse / positive regulation of inflammatory response / nuclear envelope / presynaptic membrane / early endosome membrane / postsynaptic membrane / early endosome / neuron projection / Golgi membrane / neuronal cell body / Golgi apparatus / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
N-acyl-phosphatidylethanolamine-hydrolysing phospholipase D / Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-HCZ / N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGarau, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Chem Biol / Year: 2025
Title: NAPE-PLD is target of thiazide diuretics.
Authors: Chiarugi, S. / Margheriti, F. / De Lorenzi, V. / Martino, E. / Margheritis, E.G. / Moscardini, A. / Marotta, R. / Chaves-Sanjuan, A. / Del Seppia, C. / Federighi, G. / Lapi, D. / Bandiera, T. ...Authors: Chiarugi, S. / Margheriti, F. / De Lorenzi, V. / Martino, E. / Margheritis, E.G. / Moscardini, A. / Marotta, R. / Chaves-Sanjuan, A. / Del Seppia, C. / Federighi, G. / Lapi, D. / Bandiera, T. / Rapposelli, S. / Scuri, R. / Bolognesi, M. / Garau, G.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_contact_author.email / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
B: N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,29019
Polymers91,3092
Non-polymers5,98117
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-1 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.389, 94.389, 442.325
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 57 through 71 or resid 73...
d_2ens_1(chain "B" and (resid 57 through 71 or resid 73...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTHRTHRAA57 - 7157 - 71
d_12LYSLYSPROPROAA73 - 7573 - 75
d_13ILEILEPROPROAA77 - 11577 - 115
d_14GLUGLUARGARGAA117 - 166117 - 166
d_15SERSERARGARGAA168 - 314168 - 314
d_16PHEPHELEULEUAA316 - 370316 - 370
d_17ALAALAASNASNAA372 - 388372 - 388
d_18ZNZNZNZNAC401
d_19ZNZNZNZNAD402
d_1103PE3PE3PE3PEAE403
d_111DXCDXCDXCDXCAF404
d_112DXCDXCDXCDXCAG405
d_113DXCDXCDXCDXCAH406
d_114DXCDXCDXCDXCAI407
d_115DXCDXCDXCDXCAJ408
d_21SERSERTHRTHRBB57 - 7157 - 71
d_22LYSLYSPROPROBB73 - 7573 - 75
d_23ILEILEPROPROBB77 - 11577 - 115
d_24GLUGLUARGARGBB117 - 166117 - 166
d_25SERSERARGARGBB168 - 314168 - 314
d_26PHEPHELEULEUBB316 - 370316 - 370
d_27ALAALAASNASNBB372 - 388372 - 388
d_28ZNZNZNZNBN603
d_29ZNZNZNZNBO604
d_2103PE3PE3PE3PEBP605
d_211DXCDXCDXCDXCAK409
d_212DXCDXCDXCDXCBL601
d_213DXCDXCDXCDXCBM602
d_214DXCDXCDXCDXCBQ606
d_215DXCDXCDXCDXCBR607

NCS oper: (Code: givenMatrix: (-0.457594414051, -0.877942766307, -0.140797199256), (-0.877979962222, 0.421106632606, 0.227640923191), (-0.140565067372, 0.227784334546, -0.963512199596)Vector: 44. ...NCS oper: (Code: given
Matrix: (-0.457594414051, -0.877942766307, -0.140797199256), (-0.877979962222, 0.421106632606, 0.227640923191), (-0.140565067372, 0.227784334546, -0.963512199596)
Vector: 44.4991379076, -30.2500232542, 362.034219848)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D / N-acyl phosphatidylethanolamine phospholipase D / NAPE-PLD / NAPE-hydrolyzing phospholipase D


Mass: 45654.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAPEPLD, C7orf18 / Production host: Escherichia phage EcSzw-2 (virus)
References: UniProt: Q6IQ20, N-acetylphosphatidylethanolamine-hydrolysing phospholipase D

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Non-polymers , 5 types, 55 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical
ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#5: Chemical ChemComp-HCZ / 6-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide 1,1-dioxide


Mass: 297.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8ClN3O4S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water


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

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Details

Has ligand of interestY
Has protein modificationN

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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: 60.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→88.47 Å / Num. obs: 35073 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 87.76 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.7
Reflection shellResolution: 2.86→3.02 Å / Rmerge(I) obs: 1.5 / Num. unique obs: 4539

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→54.75 Å / SU ML: 0.5135 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.9187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3011 1468 5.17 %
Rwork0.2651 26937 -
obs0.2669 28405 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.57 Å2
Refinement stepCycle: LAST / Resolution: 2.85→54.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 389 38 5884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816111
X-RAY DIFFRACTIONf_angle_d1.26128382
X-RAY DIFFRACTIONf_chiral_restr0.0678892
X-RAY DIFFRACTIONf_plane_restr0.00851019
X-RAY DIFFRACTIONf_dihedral_angle_d19.92462197
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.82148408728 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.950.51181540.46812577X-RAY DIFFRACTION98.56
2.95-3.070.43461460.42462580X-RAY DIFFRACTION99.02
3.07-3.210.38281310.35372640X-RAY DIFFRACTION99.5
3.21-3.380.3361370.33342652X-RAY DIFFRACTION99.54
3.38-3.590.351440.322628X-RAY DIFFRACTION99.53
3.59-3.870.30421360.27292672X-RAY DIFFRACTION99.57
3.87-4.260.25531510.24222697X-RAY DIFFRACTION99.93
4.26-4.870.23481410.21942727X-RAY DIFFRACTION99.86
4.87-6.130.33411600.23112765X-RAY DIFFRACTION99.97
6.14-54.750.27051680.24232999X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: -2.91861123212 Å / Origin y: 25.4107830206 Å / Origin z: 187.556216922 Å
111213212223313233
T0.921180366191 Å20.205877195543 Å20.028110544058 Å2-0.404430574264 Å2-0.052029358794 Å2--0.550016794814 Å2
L2.44905609561 °20.0461597490002 °21.04261779268 °2-0.909053585493 °20.189780647051 °2--1.93092398003 °2
S0.0182716997203 Å °0.0354099339788 Å °-0.0960513951019 Å °0.145555179622 Å °-0.0276515789406 Å °0.0214216050624 Å °-0.148105601556 Å °0.148081010159 Å °0.0367984021471 Å °
Refinement TLS groupSelection details: all

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