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- PDB-9bqx: Membrane-bound AMPH-1 tube in the presence of GTP -

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Basic information

Entry
Database: PDB / ID: 9bqx
TitleMembrane-bound AMPH-1 tube in the presence of GTP
ComponentsAmphiphysin
KeywordsLIPID BINDING PROTEIN / membrane tubulation protein complex
Function / homology
Function and homology information


lipid tube assembly involved in organelle fission / Clathrin-mediated endocytosis / Neutrophil degranulation / nucleus localization / nucleus organization / recycling endosome / phospholipid binding / nuclear envelope / perinuclear region of cytoplasm / plasma membrane
Similarity search - Function
Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsWang, Y. / Gai, W. / Zhang, J. / Rye, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Traffic / Year: 2023
Title: GTP-stimulated membrane fission by the N-BAR protein AMPH-1.
Authors: Lauren Kustigian / Xue Gong / Wei Gai / Jirapat Thongchol / Junjie Zhang / Jason Puchalla / Chavela M Carr / Hays S Rye /
Abstract: Membrane-enclosed transport carriers sort biological molecules between stations in the cell in a dynamic process that is fundamental to the physiology of eukaryotic organisms. While much is known ...Membrane-enclosed transport carriers sort biological molecules between stations in the cell in a dynamic process that is fundamental to the physiology of eukaryotic organisms. While much is known about the formation and release of carriers from specific intracellular membranes, the mechanism of carrier formation from the recycling endosome, a compartment central to cellular signaling, remains to be resolved. In Caenorhabditis elegans, formation of transport carriers from the recycling endosome requires the dynamin-like, Eps15-homology domain (EHD) protein, RME-1, functioning with the Bin/Amphiphysin/Rvs (N-BAR) domain protein, AMPH-1. Here we show, using a free-solution single-particle technique known as burst analysis spectroscopy (BAS), that AMPH-1 alone creates small, tubular-vesicular products from large, unilamellar vesicles by membrane fission. Membrane fission requires the amphipathic H0 helix of AMPH-1 and is slowed in the presence of RME-1. Unexpectedly, AMPH-1-induced membrane fission is stimulated in the presence of GTP. Furthermore, the GTP-stimulated membrane fission activity seen for AMPH-1 is recapitulated by the heterodimeric N-BAR amphiphysin protein from yeast, Rvs161/167p, strongly suggesting that GTP-stimulated membrane fission is a general property of this important class of N-BAR proteins.
History
DepositionMay 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amphiphysin
B: Amphiphysin
C: Amphiphysin
D: Amphiphysin


Theoretical massNumber of molelcules
Total (without water)109,7204
Polymers109,7204
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Amphiphysin / AMPH-1


Mass: 27430.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: amph-1, CELE_F58G6.1, F58G6.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21004
Has protein modificationN

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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: Membrane-bound AMPH-1 tube / Type: COMPLEX
Details: Membrane-bound AMPH-1 tubulation of Caenorhabditis elegans
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.17 MDa / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 50mM Tris, 300 NaCl, 1mM MgCl2, 1mM DTT
Buffer componentConc.: 50 mM / Name: Tris / Formula: C4H11NO3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 25000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -33.2 ° / Axial rise/subunit: 50.2 Å / Axial symmetry: C1
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43581 / Num. of class averages: 1 / Symmetry type: HELICAL

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