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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: Gunn, K.H. / Wheless, A. / Calcraft, T. / Kreutzberger, M. / El-Houshy, K. / Egelman, E.H. / Rosental, P.B. / Neher, S.B.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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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