[English] 日本語
Yorodumi
- EMDB-18318: Cryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18318
TitleCryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1)
Map dataPrimary sharpened map.
Sample
  • Complex: Vipp1_L1
    • Protein or peptide: Membrane-associated protein Vipp1
KeywordsVipp1/IM30/ESCRT-III / Membrane remodeling / Cryoelectron microscopy / Helical filament structure / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsNaskar S / Low HH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215553/Z/19/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mechanism for Vipp1 spiral formation, ring biogenesis, and membrane repair.
Authors: Souvik Naskar / Andrea Merino / Javier Espadas / Jayanti Singh / Aurelien Roux / Adai Colom / Harry H Low /
Abstract: The ESCRT-III-like protein Vipp1 couples filament polymerization with membrane remodeling. It assembles planar sheets as well as 3D rings and helical polymers, all implicated in mitigating plastid- ...The ESCRT-III-like protein Vipp1 couples filament polymerization with membrane remodeling. It assembles planar sheets as well as 3D rings and helical polymers, all implicated in mitigating plastid-associated membrane stress. The architecture of Vipp1 planar sheets and helical polymers remains unknown, as do the geometric changes required to transition between polymeric forms. Here we show how cyanobacterial Vipp1 assembles into morphologically-related sheets and spirals on membranes in vitro. The spirals converge to form a central ring similar to those described in membrane budding. Cryo-EM structures of helical filaments reveal a close geometric relationship between Vipp1 helical and planar lattices. Moreover, the helical structures reveal how filaments twist-a process required for Vipp1, and likely other ESCRT-III filaments, to transition between planar and 3D architectures. Overall, our results provide a molecular model for Vipp1 ring biogenesis and a mechanism for Vipp1 membrane stabilization and repair, with implications for other ESCRT-III systems.
History
DepositionAug 25, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18318.png

Downloads & links

-
Map

FileDownload / File: emd_18318.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 450 pix.
= 482.4 Å		1.07 Å/pix.
x 450 pix.
= 482.4 Å		1.07 Å/pix.
x 450 pix.
= 482.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.7
Minimum - Maximum-9.965844000000001 - 19.687235000000001
Average (Standard dev.)-0.000000000004707 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened and unmasked raw map from 3D auto-refinement.

Fileemd_18318_additional_1.map
AnnotationUnsharpened and unmasked raw map from 3D auto-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional sharpened map produced by DeepEMhancer.

Fileemd_18318_additional_2.map
AnnotationAdditional sharpened map produced by DeepEMhancer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unmasked raw half-map 1.

Fileemd_18318_half_map_1.map
AnnotationUnmasked raw half-map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unmasked raw half-map 2.

Fileemd_18318_half_map_2.map
AnnotationUnmasked raw half-map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vipp1_L1

EntireName: Vipp1_L1
Components
  • Complex: Vipp1_L1
    • Protein or peptide: Membrane-associated protein Vipp1

-
Supramolecule #1: Vipp1_L1

SupramoleculeName: Vipp1_L1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc punctiforme (bacteria)

-
Macromolecule #1: Membrane-associated protein Vipp1

MacromoleculeName: Membrane-associated protein Vipp1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc punctiforme (bacteria)
Molecular weightTheoretical: 23.9621 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLFDRIKRV VSSNLNDLVN KAEDPEKMLE QAILEMQEDL VQLRQGVAQA IAAQKRSEKQ YNDAQNEINK WQRNAQLALQ KGDENLARQ ALERKKTYTD TSAALKASLD TQSTQVETLK RNLIQLESKI SEAKTKKEML KARITTAKAQ EQLQGMVRGM N TSSAMSAF ...String:
MGLFDRIKRV VSSNLNDLVN KAEDPEKMLE QAILEMQEDL VQLRQGVAQA IAAQKRSEKQ YNDAQNEINK WQRNAQLALQ KGDENLARQ ALERKKTYTD TSAALKASLD TQSTQVETLK RNLIQLESKI SEAKTKKEML KARITTAKAQ EQLQGMVRGM N TSSAMSAF ERMEEKVLMQ ESRAQALGEL AGADLETQFA QLEGGSDVDD ELAALK

UniProtKB: Membrane-associated protein Vipp1

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1.7 mg/mL
BufferpH: 8.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.372081 Å
Applied symmetry - Helical parameters - Δ&Phi: -75.860068 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 43480
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 91.05
Output model

PDB-8qbr:
Cryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1)

+
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