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- PDB-8qbw: Cryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with ... -

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Basic information

Entry
Database: PDB / ID: 8qbw
TitleCryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with lattice 3 (Vipp1-deltaH6_L3)
ComponentsPhage shock protein A, PspA
KeywordsLIPID BINDING PROTEIN / Vipp1/IM30/ESCRT-III / Membrane remodeling / Cryoelectron microscopy / Helical filament structure
Function / homologyPspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsNaskar, S. / Low, H.H.
Funding support United Kingdom, 1items
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, H.H.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage shock protein A, PspA


Theoretical massNumber of molelcules
Total (without water)24,5031
Polymers24,5031
Non-polymers00
Water00
1
A: Phage shock protein A, PspA
x 84


Theoretical massNumber of molelcules
Total (without water)2,058,23384
Polymers2,058,23384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation83
MethodUCSF CHIMERA

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Components

#1: Protein Phage shock protein A, PspA


Mass: 24502.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R3963 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J6D9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Vipp1-deltaH6_L3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Nostoc punctiforme (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm
Image recordingAverage exposure time: 3 sec. / Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4RELION4CTF correctionCTFFIND-4.1
7UCSF ChimeraX1.5model fitting
12RELION43D reconstruction
13Cootmodel refinement
14ISOLDEmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 85.494851 ° / Axial rise/subunit: 2.159955 Å / Axial symmetry: C1
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38585 / Symmetry type: HELICAL
Atomic model buildingB value: 56.4 / Space: REAL

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