[English] 日本語
Yorodumi
- PDB-6mlu: Cryo-EM structure of lipid droplet formation protein Seipin/BSCL2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mlu
TitleCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
ComponentsSeipin
KeywordsMEMBRANE PROTEIN / Lipid storage / Lipid droplet formation / lipodystrophy
Function / homology
Function and homology information


positive regulation of axon extension involved in regeneration / diacylglycerol metabolic process / regulation of triglyceride metabolic process / phosphatidic acid metabolic process / lipid droplet formation / regulation of lipid storage / regulation of lipid biosynthetic process / channel activator activity / lipid storage / lipid droplet organization ...positive regulation of axon extension involved in regeneration / diacylglycerol metabolic process / regulation of triglyceride metabolic process / phosphatidic acid metabolic process / lipid droplet formation / regulation of lipid storage / regulation of lipid biosynthetic process / channel activator activity / lipid storage / lipid droplet organization / response to starvation / lipid catabolic process / lipid droplet / intracellular calcium ion homeostasis / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Seipin family / Putative adipose-regulatory protein (Seipin)
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsSui, X. / Arlt, H. / Liao, M. / Walther, C.T. / Farese, V.R.
Funding support United States, Germany, 6items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01GM123089 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01GM124348-01 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM097194 United States
American Heart Association18POST34030308 United States
German Research Foundation (DFG)AR1164/1-1 Germany
CitationJournal: J Cell Biol / Year: 2018
Title: Cryo-electron microscopy structure of the lipid droplet-formation protein seipin.
Authors: Xuewu Sui / Henning Arlt / Kelly P Brock / Zon Weng Lai / Frank DiMaio / Debora S Marks / Maofu Liao / Robert V Farese / Tobias C Walther /
Abstract: Metabolic energy is stored in cells primarily as triacylglycerols in lipid droplets (LDs), and LD dysregulation leads to metabolic diseases. The formation of monolayer-bound LDs from the endoplasmic ...Metabolic energy is stored in cells primarily as triacylglycerols in lipid droplets (LDs), and LD dysregulation leads to metabolic diseases. The formation of monolayer-bound LDs from the endoplasmic reticulum (ER) bilayer is poorly understood, but the ER protein seipin is essential to this process. In this study, we report a cryo-electron microscopy structure and functional characterization of seipin. The structure reveals a ring-shaped dodecamer with the luminal domain of each monomer resolved at ∼4.0 Å. Each luminal domain monomer exhibits two distinctive features: a hydrophobic helix (HH) positioned toward the ER bilayer and a β-sandwich domain with structural similarity to lipid-binding proteins. This structure and our functional testing in cells suggest a model in which seipin oligomers initially detect forming LDs in the ER via HHs and subsequently act as membrane anchors to enable lipid transfer and LD growth.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 17, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / 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 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.6Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-9146
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9146
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Seipin
B: Seipin


Theoretical massNumber of molelcules
Total (without water)87,9142
Polymers87,9142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Negative staining electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area17750 Å2

-
Components

#1: Protein Seipin


Mass: 43957.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Seipin, CG9904 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V3X4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: cryo-EM protein structure of seipin/BSCL2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 43 kDa/nm / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET28a
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Protein sample was monodisperse.
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 58 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D12 (2x12 fold dihedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22383 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0052584
ELECTRON MICROSCOPYf_angle_d1.0183502
ELECTRON MICROSCOPYf_dihedral_angle_d4.3831574
ELECTRON MICROSCOPYf_chiral_restr0.064388
ELECTRON MICROSCOPYf_plane_restr0.007442

+
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