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- EMDB-18318: Cryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1) -

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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: To Be Published
Title: Mechanism for Vipp1 spiral formation, ring biogenesis and membrane repair.
Authors: Naskar S / Merino A / Espadas J / Singh J / Roux A / Colom A / Low HH
History
DepositionAug 25, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18318.png

Downloads & links

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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 °

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Supplemental data

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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)

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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)

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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)

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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)

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Sample components

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Entire : Vipp1_L1

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

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Supramolecule #1: Vipp1_L1

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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

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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

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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)

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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)

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