[English] 日本語
Yorodumi
- EMDB-71426: Unknown entry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71426
TitleLipid droplet biogenesis by the seipin complex
Map dataLipid droplet biogenesis by the seipin complex
Sample
  • Complex: Seipin
    • Protein or peptide: Seipin
KeywordsComplex / endoplasmic reticulum / lipid droplet / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPedro CM / Siyoung K / Yohannes A / Gregory V / Tobias W / Robert F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124348 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Lipid droplet biogenesis by the seipin complex
Authors: Pedro CM / Siyoung K / Yohannes A / Gregory V / Tobias W / Robert F
History
DepositionJun 25, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71426.png

Downloads & links

-
Map

FileReleased
AnnotationLipid droplet biogenesis by the seipin complex
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-1.8832257 - 2.4679556
Average (Standard dev.)0.00020309116 (±0.019401055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 552.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Seipin

EntireName: Seipin
Components
  • Complex: Seipin
    • Protein or peptide: Seipin

-
Supramolecule #1: Seipin

SupramoleculeName: Seipin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Seipin

MacromoleculeName: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 38.456801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLLMFLRAR RIFLQAAILL CVLLLLLWVS VFLYGSFYYS YMPTVKYSSP VHYQYSSTCE PPPGILCSFP MANVSLLRNN RDRVLMHGQ PYRISLELQL PESIVNQDLG MFMVTMSCYT RGGRQISYTA RSAMLHYKSP LLRTMETMAS SPLLLLGLSD Q KQILEVEL ...String:
MGLLMFLRAR RIFLQAAILL CVLLLLLWVS VFLYGSFYYS YMPTVKYSSP VHYQYSSTCE PPPGILCSFP MANVSLLRNN RDRVLMHGQ PYRISLELQL PESIVNQDLG MFMVTMSCYT RGGRQISYTA RSAMLHYKSP LLRTMETMAS SPLLLLGLSD Q KQILEVEL YSEYREDSYV PTVGAVIQIQ SVRIQIYSAE LRVHAYFTGL RYLLYNFPIT SAVIGISSNF IFLSVLVLLS YL QWGFGRT RLQDVQEWTR DVRRADTRPE SVSQTDDKDQ PDTETIGQND TDSQGAPQTD EDTQVVQNIS ADMETESSSQ FSV LRHRST EQKLISEEDL

UniProtKB: berardinelli-Seip congenital lipodystrophy 2 (Seipin) L homeolog isoform X1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.29 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Software - details: Single particle / Number images used: 646025
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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