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- PDB-9nrn: Lipoprotein Lipase Helical Filament with 11 nm diameter -

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Basic information

Entry
Database: PDB / ID: 9nrn
TitleLipoprotein Lipase Helical Filament with 11 nm diameter
ComponentsLipoprotein lipase
KeywordsHYDROLASE / Lipase / Filament / Helical Complex
Function / homology
Function and homology information


Assembly of active LPL and LIPC lipase complexes / Chylomicron remodeling / Retinoid metabolism and transport / lipoprotein lipase / low-density lipoprotein particle mediated signaling / lipoprotein lipase activity / chylomicron remodeling / positive regulation of cholesterol storage / phospholipase A1 / phospholipase activity ...Assembly of active LPL and LIPC lipase complexes / Chylomicron remodeling / Retinoid metabolism and transport / lipoprotein lipase / low-density lipoprotein particle mediated signaling / lipoprotein lipase activity / chylomicron remodeling / positive regulation of cholesterol storage / phospholipase A1 / phospholipase activity / phospholipase A1 activity / triglyceride catabolic process / very-low-density lipoprotein particle remodeling / very-low-density lipoprotein particle clearance / chylomicron / cellular response to nutrient / high-density lipoprotein particle remodeling / triacylglycerol lipase activity / very-low-density lipoprotein particle / heparan sulfate proteoglycan binding / cellular response to fatty acid / positive regulation of macrophage derived foam cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / triglyceride homeostasis / triglyceride metabolic process / lipoprotein particle binding / apolipoprotein binding / catalytic complex / positive regulation of fat cell differentiation / response to glucose / retinoid metabolic process / phospholipid metabolic process / positive regulation of adipose tissue development / cholesterol homeostasis / positive regulation of interleukin-1 beta production / response to bacterium / positive regulation of interleukin-6 production / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / fatty acid biosynthetic process / heparin binding / signaling receptor binding / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / plasma membrane
Similarity search - Function
Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain ...Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGunn, K.H. / Wheless, A. / Neher, S.B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL125654 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL163352 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM146024-04 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Sci Adv / Year: 2025
Title: Cryogenic electron tomography reveals helical organization of lipoprotein lipase in storage vesicles.
Authors: Kathryn H Gunn / Anna Wheless / Thomas Calcraft / Mark Kreutzberger / Kareem El-Houshy / Edward H Egelman / Peter B Rosenthal / Saskia B Neher /
Abstract: Lipoprotein lipase (LPL) is a triglyceride lipase that is contained in intracellular vesicles in an inactive storage form before secretion, but the precise structural details have not yet been ...Lipoprotein lipase (LPL) is a triglyceride lipase that is contained in intracellular vesicles in an inactive storage form before secretion, but the precise structural details have not yet been resolved. Using cryo-electron tomography (cryo-ET), we observe that LPL exists inside of storage vesicles as a filament with an 11-nanometer diameter and is packed in these vesicles in two distinct patterns. Next, we solved a 4.2-Å resolution cryo-electron microscopy (cryo-EM) structure of this 11-nanometer LPL filament using purified protein. The filament is made of repeating pairs of LPL molecules with occluded active sites, rendering the LPL inactive. The comparison of the in situ subtomogram average and the in vitro cryo-EM structure indicates that the previously uncharacterized physiological storage form of LPL is an inactive filament.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein lipase
B: Lipoprotein lipase
C: Lipoprotein lipase
D: Lipoprotein lipase
E: Lipoprotein lipase
F: Lipoprotein lipase
G: Lipoprotein lipase
H: Lipoprotein lipase
I: Lipoprotein lipase
J: Lipoprotein lipase
K: Lipoprotein lipase
L: Lipoprotein lipase
M: Lipoprotein lipase
N: Lipoprotein lipase
O: Lipoprotein lipase
P: Lipoprotein lipase
Q: Lipoprotein lipase
R: Lipoprotein lipase


Theoretical massNumber of molelcules
Total (without water)880,22618
Polymers880,22618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Lipoprotein lipase / LPL / Phospholipase A1


Mass: 48901.438 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Plasmid details: Milk
References: UniProt: P11151, lipoprotein lipase, phospholipase A1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical filament of lipoprotein lipase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.4 / Details: 20 mM HEPES pH 7.4 500 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 250 nm / Cs: 2.7 mm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2952

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
7Coot0.9.5model fitting
9PHENIX1.20.1model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -65.95 ° / Axial rise/subunit: 23.7 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 251000
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 6U7M

6u7m


Pdb chain-ID: c / Accession code: 6U7M / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 103.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00463486
ELECTRON MICROSCOPYf_angle_d0.596485986
ELECTRON MICROSCOPYf_chiral_restr0.03829234
ELECTRON MICROSCOPYf_plane_restr0.003711034
ELECTRON MICROSCOPYf_dihedral_angle_d13.88423148

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