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- EMDB-20673: Cryo-EM Structure of Helical Lipoprotein Lipase -

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Basic information

Entry
Database: EMDB / ID: EMD-20673
TitleCryo-EM Structure of Helical Lipoprotein Lipase
Map dataHelical Lipoprotein Lipase
Sample
  • Complex: filament of lipoprotein lipase
    • Protein or peptide: Lipoprotein lipase
Keywordshelical symmetry / lipoprotein lipase / PROTEIN FIBRIL / HYDROLASE
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGunn KH / Wang F
Funding support United States, 2 items
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, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseApr 8, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0118
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0118
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6u7m
  • Surface level: 0.0118
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6u7m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20673.png

Downloads & links

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Map

FileDownload / File: emd_20673.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical Lipoprotein Lipase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.773 Å		0.93 Å/pix.
x 384 pix.
= 357.773 Å		0.93 Å/pix.
x 384 pix.
= 357.773 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9317 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0118 / Movie #1: 0.0118
Minimum - Maximum-0.018342389 - 0.045466844
Average (Standard dev.)0.00046269008 (±0.003622726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 357.7728 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.931700520833330.931700520833330.93170052083333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z357.773357.773357.773
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.0180.0450.000

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Supplemental data

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Sample components

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Entire : filament of lipoprotein lipase

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

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Supramolecule #1: filament of lipoprotein lipase

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

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Macromolecule #1: Lipoprotein lipase

MacromoleculeName: Lipoprotein lipase / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO / EC number: lipoprotein lipase
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 53.448789 KDa
SequenceString: MESKALLLLA LSVCLQSLTV SRGGLVAADR ITGGKDFRDI ESKFALRTPE DTAEDTCHLI PGVTESVANC HFNHSSKTFV VIHGWTVTG MYESWVPKLV AALYKREPDS NVIVVDWLSR AQQHYPVSAG YTKLVGQDVA KFMNWMADEF NYPLGNVHLL G YSLGAHAA ...String:
MESKALLLLA LSVCLQSLTV SRGGLVAADR ITGGKDFRDI ESKFALRTPE DTAEDTCHLI PGVTESVANC HFNHSSKTFV VIHGWTVTG MYESWVPKLV AALYKREPDS NVIVVDWLSR AQQHYPVSAG YTKLVGQDVA KFMNWMADEF NYPLGNVHLL G YSLGAHAA GIAGSLTNKK VNRITGLDPA GPNFEYAEAP SRLSPDDADF VDVLHTFTRG SPGRSIGIQK PVGHVDIYPN GG TFQPGCN IGEALRVIAE RGLGDVDQLV KCSHERSVHL FIDSLLNEEN PSKAYRCNSK EAFEKGLCLS CRKNRCNNMG YEI NKVRAK RSSKMYLKTR SQMPYKVFHY QVKIHFSGTE SNTYTNQAFE ISLYGTVAES ENIPFTLPEV STNKTYSFLL YTEV DIGEL LMLKLKWISD SYFSWSNWWS SPGFDIGKIR VKAGETQKKV IFCSREKMSY LQKGKSPVIF VKCHDKSLNR KSG

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

Concentration0.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.875 MNaClSodium Chloride
2.5 %C3H8O3Glycerol
2.5 mMC8H19NO5Bis-Tris pH 6.5
15.0 mMC4H11NO3Tris HCl pH 8
GridPretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 15 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: Blot 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1764 / Average exposure time: 12.8 sec. / Average electron dose: 46.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 10.88 Å
Applied symmetry - Helical parameters - Δ&Phi: 130.05 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.0)
Details: model: map FSC 0.38 cutoff; map: map FSC 0.143 cutoff
Number images used: 108911
Segment selectionNumber selected: 157128
Software:
Namedetails
RELION (ver. 3.0)
EMAN2 (ver. 2.21)e2helixboxer.py
Startup modelType of model: OTHER
Details: 127 A radius featureless cylinder generated in RELION
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

Initial modelPDB ID:

6e7k


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

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

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