[English] 日本語
Yorodumi
- EMDB-20673: Cryo-EM Structure of Helical Lipoprotein Lipase -

+
Open data


ID or keywords:

Loading...

-
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
Function / homology
Function and homology information


Assembly of active LPL and LIPC lipase complexes / positive regulation of chemokine production => GO:0032722 / lipoprotein lipase / lipoprotein lipase activity / positive regulation of tumor necrosis factor production => GO:0032760 / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / positive regulation of cholesterol storage / phospholipase A1 ...Assembly of active LPL and LIPC lipase complexes / positive regulation of chemokine production => GO:0032722 / lipoprotein lipase / lipoprotein lipase activity / positive regulation of tumor necrosis factor production => GO:0032760 / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / positive regulation of cholesterol storage / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase activity / triglyceride catabolic process / lipase activity / very-low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / chylomicron / cellular response to nutrient / very-low-density lipoprotein particle / triglyceride lipase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / heparan sulfate proteoglycan binding / triglyceride homeostasis / cellular response to fatty acid / triglyceride metabolic process / lipoprotein particle binding / apolipoprotein binding / positive regulation of fat cell differentiation / phospholipid metabolic process / response to glucose / lipid catabolic process / positive regulation of interleukin-1 beta production / cholesterol homeostasis / response to bacterium / fatty acid biosynthetic process / positive regulation of inflammatory response / positive regulation of interleukin-6 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) / Bovine (cattle)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGunn KH / Wang F / Egelman EH / Neher SB
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-
UpdateMay 27, 2020-
Current statusMay 27, 2020Processing site: RCSB / Status: Released

-
Structure visualization

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

emd_20673.png

Downloads & links

-
Map

FileDownload / File: emd_20673.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical Lipoprotein Lipase
Voxel sizeX=Y=Z: 0.9317 Å
Density
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

-
Supplemental data

-
Sample components

-
Entire : filament of lipoprotein lipase

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

-
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)

-
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: Bovine (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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.875 MNaClSodium chlorideSodium Chloride
2.5 %C3H8O3Glycerol
2.5 mMC8H19NO5Bis-Tris pH 6.5
15.0 mMC4H11NO3Tris HCl pH 8
GridPretreatment - Type: PLASMA CLEANING / 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.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 157128
Software:
Namedetails
RELION (ver. 3.0)
EMAN2 (ver. 2.21)e2helixboxer.py
CTF correctionSoftware - Name: CTFFIND (ver. 4)
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)
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

-
Atomic model buiding 1

Initial modelPDB ID:

6e7k


Chain - Chain ID: A
RefinementSpace: REAL
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more