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- PDB-6q42: Crystal Structure of Human Pancreatic Phospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 6q42
TitleCrystal Structure of Human Pancreatic Phospholipase A2
ComponentsPhospholipase A2
KeywordsHYDROLASE / pancreatic phospholipase / immunomodulator
Function / homology
Function and homology information


Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / activation of phospholipase A2 activity / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process ...Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / activation of phospholipase A2 activity / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / innate immune response in mucosa / positive regulation of interleukin-8 production / positive regulation of protein secretion / actin filament organization / positive regulation of MAP kinase activity / phospholipid binding / fatty acid biosynthetic process / cellular response to insulin stimulus / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of immune response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / defense response to Gram-positive bacterium / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaul, F. / Haouz, A. / Lambeau, G. / Theze, J.
CitationJournal: J.Clin.Invest. / Year: 2020
Title: PLA2G1B is involved in CD4 anergy and CD4 lymphopenia in HIV-infected patients.
Authors: Pothlichet, J. / Rose, T. / Bugault, F. / Jeammet, L. / Meola, A. / Haouz, A. / Saul, F. / Geny, D. / Alcami, J. / Ruiz-Mateos, E. / Teyton, L. / Lambeau, G. / Theze, J.
History
DepositionDec 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4566
Polymers28,3142
Non-polymers1424
Water6,107339
1
A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2283
Polymers14,1571
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2283
Polymers14,1571
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-47 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.610, 58.951, 122.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phospholipase A2 / Group IB phospholipase A2 / Phosphatidylcholine 2-acylhydrolase 1B


Mass: 14157.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G1B, PLA2, PLA2A, PPLA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04054, phospholipase A2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 32% (w/v) PEG4K, 0.8M Lithium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07184 Å / Relative weight: 1
ReflectionResolution: 1.9→42.2 Å / Num. obs: 18069 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 1.9 / % possible all: 98

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B00

2b00


Resolution: 1.9→42 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.225 --
Rwork0.175 --
obs-18016 99.2 %
Refinement stepCycle: LAST / Resolution: 1.9→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 4 339 2301

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