[English] 日本語
Yorodumi
- EMDB-49737: Subtomogram Average of in situ Lipoprotein Lipase Filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49737
TitleSubtomogram Average of in situ Lipoprotein Lipase Filament
Map dataSubtomogram average of human Lipoprotein Lipase from images taken of vesicles presenting gold-labeled syndecan-1. B factor of 1000 applied during post-processing.
Sample
  • Complex: Lipoprotein Lipase Filament found in Vesicles
KeywordsLipase / Filament / Helical Complex / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsGunn KH / Wheless A / Neher SB
Funding support United States, 3 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
CitationJournal: Sci Adv / Year: 2025
Title: Cryogenic electron tomography reveals helical organization of lipoprotein lipase in storage vesicles.
Authors: Kathryn H Gunn / Anna Wheless / Thomas Calcraft / Mark Kreutzberger / Kareem El-Houshy / Edward H Egelman / Peter B Rosenthal / Saskia B Neher /
Abstract: Lipoprotein lipase (LPL) is a triglyceride lipase that is contained in intracellular vesicles in an inactive storage form before secretion, but the precise structural details have not yet been ...Lipoprotein lipase (LPL) is a triglyceride lipase that is contained in intracellular vesicles in an inactive storage form before secretion, but the precise structural details have not yet been resolved. Using cryo-electron tomography (cryo-ET), we observe that LPL exists inside of storage vesicles as a filament with an 11-nanometer diameter and is packed in these vesicles in two distinct patterns. Next, we solved a 4.2-Å resolution cryo-electron microscopy (cryo-EM) structure of this 11-nanometer LPL filament using purified protein. The filament is made of repeating pairs of LPL molecules with occluded active sites, rendering the LPL inactive. The comparison of the in situ subtomogram average and the in vitro cryo-EM structure indicates that the previously uncharacterized physiological storage form of LPL is an inactive filament.
History
DepositionMar 14, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49737.png

Downloads & links

-
Map

FileDownload / File: emd_49737.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of human Lipoprotein Lipase from images taken of vesicles presenting gold-labeled syndecan-1. B factor of 1000 applied during post-processing.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 256 pix.
= 503.04 Å		1.97 Å/pix.
x 256 pix.
= 503.04 Å		1.97 Å/pix.
x 256 pix.
= 503.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.965 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00854
Minimum - Maximum-0.06017094 - 0.15254377
Average (Standard dev.)0.00054924283 (±0.004803483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 503.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_49737_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unfiltered and unweighted reconstruction, lowpass filtered to 32...

Fileemd_49737_additional_1.map
AnnotationUnfiltered and unweighted reconstruction, lowpass filtered to 32 Angstroms.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered and unweighted half map (2/2).

Fileemd_49737_half_map_1.map
AnnotationUnfiltered and unweighted half map (2/2).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered and unweighted half map (1/2).

Fileemd_49737_half_map_2.map
AnnotationUnfiltered and unweighted half map (1/2).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lipoprotein Lipase Filament found in Vesicles

EntireName: Lipoprotein Lipase Filament found in Vesicles
Components
  • Complex: Lipoprotein Lipase Filament found in Vesicles

-
Supramolecule #1: Lipoprotein Lipase Filament found in Vesicles

SupramoleculeName: Lipoprotein Lipase Filament found in Vesicles / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.2 / Details: 20 mM HEPES pH 7.2 5% Sorbitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE-PROPANE
DetailsPurified vesicles from HEK293 cells overexpressing lipoprotein lipase and syndecan-1

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 2452
ExtractionNumber tomograms: 19 / Number images used: 8155 / Software - Name: RELION (ver. 4.0.1)
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

+
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