[English] 日本語
Yorodumi
- EMDB-18423: C12 Vipp1 stacked rings in the presence of EPL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18423
TitleC12 Vipp1 stacked rings in the presence of EPL
Map data
Sample
  • Complex: Vipp1
    • Protein or peptide: Vipp1
Keywordsmembrane tubulation / membrane remodeling / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsJunglas B / Sachse B
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SA 1882/6-1 Germany
German Research Foundation (DFG)SCHN 690/16-1 Germany
Citation
Journal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies.
Authors: Benedikt Junglas / David Kartte / Mirka Kutzner / Nadja Hellmann / Ilona Ritter / Dirk Schneider / Carsten Sachse /
Abstract: Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting ...Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting complexes required for transport III superfamily, it is still unknown how Vipp1 remodels membranes. Here, we present cryo-electron microscopy structures of Synechocystis Vipp1 interacting with membranes: seven structures of helical and stacked-ring assemblies at 5-7-Å resolution engulfing membranes and three carpet structures covering lipid vesicles at ~20-Å resolution using subtomogram averaging. By analyzing ten structures of N-terminally truncated Vipp1, we show that helix α0 is essential for membrane tubulation and forms the membrane-anchoring domain of Vipp1. Lastly, using a conformation-restrained Vipp1 mutant, we reduced the structural plasticity of Vipp1 and determined two structures of Vipp1 at 3.0-Å resolution, resolving the molecular details of membrane-anchoring and intersubunit contacts of helix α0. Our data reveal membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.
#1: Journal: Biorxiv / Year: 2024
Title: Structural basis for Vipp1 membrane binding: From loose coats and carpets to ring and rod assemblies
Authors: Junglas B / Kartte D / Kutzner M / Hellmann N / Ritter I / Schneider D / Sachse C
History
DepositionSep 11, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18423.png

Downloads & links

-
Map

FileDownload / File: emd_18423.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 400 pix.
= 520. Å		1.3 Å/pix.
x 400 pix.
= 520. Å		1.3 Å/pix.
x 400 pix.
= 520. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0954
Minimum - Maximum-0.11675465 - 0.4585682
Average (Standard dev.)0.009010697 (±0.031874828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 520.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_18423_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vipp1

EntireName: Vipp1
Components
  • Complex: Vipp1
    • Protein or peptide: Vipp1

-
Supramolecule #1: Vipp1

SupramoleculeName: Vipp1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

-
Macromolecule #1: Vipp1

MacromoleculeName: Vipp1 / type: protein_or_peptide / ID: 1 / Details: Vipp1 with EPL lipid / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGLFDRLGRV VRANLNDLVS KAEDPEKVLE QAVIDMQEDL VQLRQAVART IAEEKRTEQR LNQDTQEAKK WEDRAKLALT NGEENLAREA LARKKSLTDT AAAYQTQLAQ QRTMSENLRR NLAALEAKIS EAKTKKNMLQ ARAKAAKANA ELQQTLGGLG TSSATSAFER ...String:
MGLFDRLGRV VRANLNDLVS KAEDPEKVLE QAVIDMQEDL VQLRQAVART IAEEKRTEQR LNQDTQEAKK WEDRAKLALT NGEENLAREA LARKKSLTDT AAAYQTQLAQ QRTMSENLRR NLAALEAKIS EAKTKKNMLQ ARAKAAKANA ELQQTLGGLG TSSATSAFER MENKVLDMEA TSQAAGELAG FGIENQFAQL EASSGVEDEL AALKASMAGG ALPGTSAATP QLEAAPVDSS VPANNASQDD AVIDQELDDL RRRLNNLAAL EVLFQGP

UniProtKB: Membrane-associated protein Vipp1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59515
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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