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- EMDB-44828: Membrane-bound AMPH-1 tube in the presence of GTP -

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Basic information

Entry
Database: EMDB / ID: EMD-44828
TitleMembrane-bound AMPH-1 tube in the presence of GTP
Map data
Sample
  • Complex: Membrane-bound AMPH-1 tube
    • Protein or peptide: Amphiphysin
Keywordsmembrane tubulation protein complex / LIPID BINDING PROTEIN
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)
Methodhelical reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsWang Y / Gai W / Zhang J / Rye H
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44828.png

Downloads & links

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Map

FileDownload / File: emd_44828.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0627
Minimum - Maximum-0.10483692 - 0.17351389
Average (Standard dev.)0.0044093383 (±0.021613186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44828_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44828_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-bound AMPH-1 tube

EntireName: Membrane-bound AMPH-1 tube
Components
  • Complex: Membrane-bound AMPH-1 tube
    • Protein or peptide: Amphiphysin

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Supramolecule #1: Membrane-bound AMPH-1 tube

SupramoleculeName: Membrane-bound AMPH-1 tube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Membrane-bound AMPH-1 tubulation of Caenorhabditis elegans
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Amphiphysin

MacromoleculeName: Amphiphysin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 27.430049 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADLFNKHLK KATNRTKEKL LEGIGKAKAT QDEVFDQHAA NLNKQSKSCE KLHKDVKNYS SALRTLLSAE KQLRDTIRDA YEPEWPDRE HLTAIFDNLD IQTNELEKTV CDDLPQTVTQ YVNQFPDLKK KIEKRGRKLV DYDSAKNSFN SVKASSKKDN D PKLAKATM ...String:
MADLFNKHLK KATNRTKEKL LEGIGKAKAT QDEVFDQHAA NLNKQSKSCE KLHKDVKNYS SALRTLLSAE KQLRDTIRDA YEPEWPDRE HLTAIFDNLD IQTNELEKTV CDDLPQTVTQ YVNQFPDLKK KIEKRGRKLV DYDSAKNSFN SVKASSKKDN D PKLAKATM ELQAAEQMYT EMNNELLEIL PAVFDSRITF FVDTLQTLFN ANSVYQTDAS KFHKQIVMQL DKLGESMDYL

UniProtKB: Amphiphysin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 50.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris / Details: 50mM Tris, 300 NaCl, 1mM MgCl2, 1mM DTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 50.2 Å
Applied symmetry - Helical parameters - Δ&Phi: -33.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43581
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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