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- EMDB-49738: Lipoprotein Lipase Helical Filament with 11 nm diameter -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49738
TitleLipoprotein Lipase Helical Filament with 11 nm diameter
Map data
Sample
  • Complex: Helical filament of lipoprotein lipase
    • Protein or peptide: Lipoprotein lipase
KeywordsLipase / Filament / Helical Complex / HYDROLASE
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)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGunn KH / Wheless A / Neher SB
Funding support United States, 4 items
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 KH / Wheless A / Calcraft T / Kreutzberger M / El-Houshy K / Egelman EH / Rosental PB / Neher SB
History
DepositionMar 14, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49738.png

Downloads & links

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Map

FileDownload / File: emd_49738.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 512 pix.
= 448.512 Å		0.88 Å/pix.
x 512 pix.
= 448.512 Å		0.88 Å/pix.
x 512 pix.
= 448.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.3041935 - 0.5605971
Average (Standard dev.)0.00019890277 (±0.025336195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 448.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49738_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49738_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49738_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical filament of lipoprotein lipase

EntireName: Helical filament of lipoprotein lipase
Components
  • Complex: Helical filament of lipoprotein lipase
    • Protein or peptide: Lipoprotein lipase

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Supramolecule #1: Helical filament of lipoprotein lipase

SupramoleculeName: Helical filament of lipoprotein lipase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Lipoprotein lipase

MacromoleculeName: Lipoprotein lipase / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO / EC number: lipoprotein lipase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 48.901438 KDa
SequenceString: DFRDIESKFA LRTPEDTAED TCHLIPGVTE SVANCHFNHS SKTFVVIHGW TVTGMYESWV PKLVAALYKR EPDSNVIVVD WLSRAQQHY PVSAGYTKLV GQDVAKFMNW MADEFNYPLG NVHLLGYSLG AHAAGIAGSL TNKKVNRITG LDPAGPNFEY A EAPSRLSP ...String:
DFRDIESKFA LRTPEDTAED TCHLIPGVTE SVANCHFNHS SKTFVVIHGW TVTGMYESWV PKLVAALYKR EPDSNVIVVD WLSRAQQHY PVSAGYTKLV GQDVAKFMNW MADEFNYPLG NVHLLGYSLG AHAAGIAGSL TNKKVNRITG LDPAGPNFEY A EAPSRLSP DDADFVDVLH TFTRGSPGRS IGIQKPVGHV DIYPNGGTFQ PGCNIGEALR VIAERGLGDV DQLVKCSHER SV HLFIDSL LNEENPSKAY RCNSKEAFEK GLCLSCRKNR CNNMGYEINK VRAKRSSKMY LKTRSQMPYK VFHYQVKIHF SGT ESNTYT NQAFEISLYG TVAESENIPF TLPEVSTNKT YSFLLYTEVD IGELLMLKLK WISDSYFSWS NWWSSPGFDI GKIR VKAGE TQKKVIFCSR EKMSYLQKGK SPVIFVKCH

UniProtKB: Lipoprotein lipase

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: 20 mM HEPES pH 7.4 500 mM NaCl
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2952 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.25 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 23.7 Å
Applied symmetry - Helical parameters - Δ&Phi: -65.95 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45000
CTF correctionType: NONE
Segment selectionNumber selected: 251000 / Software - Name: cryoSPARC
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6u7m


Chain - Chain ID: c / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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