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- PDB-6u7m: Cryo-EM Structure of Helical Lipoprotein Lipase -

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Basic information

Entry
Database: PDB / ID: 6u7m
TitleCryo-EM Structure of Helical Lipoprotein Lipase
ComponentsLipoprotein lipase
KeywordsPROTEIN FIBRIL / HYDROLASE / helical symmetry / lipoprotein lipase
Function / homology
Function and homology information


Assembly of active LPL and LIPC lipase complexes / Chylomicron remodeling / Retinoid metabolism and transport / lipoprotein lipase / lipoprotein lipase activity / positive regulation of triglyceride storage / low-density lipoprotein particle mediated signaling / chylomicron remodeling / positive regulation of cholesterol storage / : ...Assembly of active LPL and LIPC lipase complexes / Chylomicron remodeling / Retinoid metabolism and transport / lipoprotein lipase / lipoprotein lipase activity / positive regulation of triglyceride storage / low-density lipoprotein particle mediated signaling / chylomicron remodeling / positive regulation of cholesterol storage / : / phospholipase A1 / : / phospholipase A1 activity / phospholipase activity / triglyceride catabolic process / very-low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / high-density lipoprotein particle remodeling / chylomicron / cellular response to nutrient / triacylglycerol lipase activity / very-low-density lipoprotein particle / heparan sulfate proteoglycan binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / triglyceride homeostasis / cellular response to fatty acid / triglyceride metabolic process / lipoprotein particle binding / apolipoprotein binding / positive regulation of fat cell differentiation / response to glucose / catalytic complex / positive regulation of adipose tissue development / phospholipid metabolic process / cholesterol homeostasis / positive regulation of interleukin-1 beta production / response to bacterium / positive regulation of interleukin-6 production / positive regulation of inflammatory response / fatty acid biosynthetic process / positive regulation of tumor necrosis factor production / 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 (cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGunn, K.H. / Wang, F. / Egelman, E.H. / Neher, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-HL12565 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35-GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: The structure of helical lipoprotein lipase reveals an unexpected twist in lipase storage.
Authors: Kathryn H Gunn / Benjamin S Roberts / Fengbin Wang / Joshua D Strauss / Mario J Borgnia / Edward H Egelman / Saskia B Neher /
Abstract: Lipases are enzymes necessary for the proper distribution and utilization of lipids in the human body. Lipoprotein lipase (LPL) is active in capillaries, where it plays a crucial role in preventing ...Lipases are enzymes necessary for the proper distribution and utilization of lipids in the human body. Lipoprotein lipase (LPL) is active in capillaries, where it plays a crucial role in preventing dyslipidemia by hydrolyzing triglycerides from packaged lipoproteins. Thirty years ago, the existence of a condensed and inactive LPL oligomer was proposed. Although recent work has shed light on the structure of the LPL monomer, the inactive oligomer remained opaque. Here we present a cryo-EM reconstruction of a helical LPL oligomer at 3.8-Å resolution. Helix formation is concentration-dependent, and helices are composed of inactive dihedral LPL dimers. Heparin binding stabilizes LPL helices, and the presence of substrate triggers helix disassembly. Superresolution fluorescent microscopy of endogenous LPL revealed that LPL adopts a filament-like distribution in vesicles. Mutation of one of the helical LPL interaction interfaces causes loss of the filament-like distribution. Taken together, this suggests that LPL is condensed into its inactive helical form for storage in intracellular vesicles.
History
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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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
S: Lipoprotein lipase
T: Lipoprotein lipase
U: Lipoprotein lipase
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


Theoretical massNumber of molelcules
Total (without water)1,603,46430
Polymers1,603,46430
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51020 Å2
ΔGint-294 kcal/mol
Surface area593230 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 10.88 Å / Rotation per n subunits: 130.05 °)
DetailsHelical parameters can be applied to chains A and a to generate the full helical assembly.

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Components

#1: Protein ...
Lipoprotein lipase / LPL


Mass: 53448.789 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P11151, lipoprotein lipase
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: filament of lipoprotein lipase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
10.875 MSodium ChlorideNaCl1
22.5 %GlycerolC3H8O31
32.5 mMBis-Tris pH 6.5C8H19NO51
415 mMTris HCl pH 8C4H11NO31
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA current
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 295 K / Details: Blot 3 seconds before plunging

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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 magnification: 45000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 12.8 sec. / Electron dose: 46.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1764
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION3particle selection
2EMAN22.21particle selectione2helixboxer.py
5CTFFIND4CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 130.05 ° / Axial rise/subunit: 10.88 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 157128
3D reconstructionResolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 108911 / Algorithm: BACK PROJECTION
Details: model: map FSC 0.38 cutoff; map: map FSC 0.143 cutoff
Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6E7K

6e7k


Pdb chain-ID: A / Accession code: 6E7K / Source name: PDB / Type: experimental model

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