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- EMDB-40946: Cryo-EM of the GDP-bound human dynamin (full-length) polymer asse... -

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Entry
Database: EMDB / ID: EMD-40946
TitleCryo-EM of the GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix)
Map dataGDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix)
Sample
  • Complex: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane (full helix)
    • Protein or peptide: Dynamin-1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsdynamin / membrane / fission / lipid / tubule / scission / endocytosis / HYDROLASE
Function / homology
Function and homology information


clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / endosome organization ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / endosome organization / Formation of annular gap junctions / photoreceptor ribbon synapse / Gap junction degradation / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / GDP binding / Clathrin-mediated endocytosis / presynapse / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsJimah JR / Canagarajah BJ / Hinshaw JE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIADK060100 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140220 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM140220 United States
CitationJournal: Dev Cell / Year: 2024
Title: Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.
Authors: John R Jimah / Nidhi Kundu / Abigail E Stanton / Kem A Sochacki / Bertram Canagarajah / Lieza Chan / Marie-Paule Strub / Huaibin Wang / Justin W Taraska / Jenny E Hinshaw /
Abstract: Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the ...Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
History
DepositionJun 1, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40946.png

Downloads & links

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Map

FileDownload / File: emd_40946.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 500 pix.
= 644.5 Å		1.29 Å/pix.
x 500 pix.
= 644.5 Å		1.29 Å/pix.
x 500 pix.
= 644.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.289 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0684
Minimum - Maximum-0.33975187 - 0.77280617
Average (Standard dev.)0.008777039 (±0.034184743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 644.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40946_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half Map 1

Fileemd_40946_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_40946_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
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Sample components

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Entire : GDP-bound human dynamin (full-length) helical polymer assembled o...

EntireName: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane (full helix)
Components
  • Complex: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane (full helix)
    • Protein or peptide: Dynamin-1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: GDP-bound human dynamin (full-length) helical polymer assembled o...

SupramoleculeName: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane (full helix)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.7 kDa/nm

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Macromolecule #1: Dynamin-1

MacromoleculeName: Dynamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.825742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAHHHHHHTG MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGASSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTE YAEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP P DIEFQIRD ...String:
MAHHHHHHTG MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGASSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTE YAEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP P DIEFQIRD MLMQFVTKEN CLILAVSPAN SDLANSDALK VAKEVDPQGQ RTIGVITKLD LMDEGTDARD VLENKLLPLR RG YIGVVNR SQKDIDGKKD ITAALAAERK FFLSHPSYRH LADRMGTPYL QKVLNQQLTN HIRDTLPGLR NKLQSQLLSI EKE VEEYKN FRPDDPARKT KALLQMVQQF AVDFEKRIEG SGDQIDTYEL SGGARINRIF HERFPFELVK MEFDEKELRR EISY AIKNI HGIRTGLFTP DMAFETIVKK QVKKIREPCL KCVDMVISEL ISTVRQCTKK LQQYPRLREE MERIVTTHIR EREGR TKEQ VMLLIDIELA YMNTNHEDFI GFANAQQRSN QMNKKKTSGN QDEILVIRKG WLTINNIGIM KGGSKEYWFV LTAENL SWY KDDEEKEKKY MLSVDNLKLR DVEKGFMSSK HIFALFNTEQ RNVYKDYRQL ELACETQEEV DSWKASFLRA GVYPERV GD KEKASETEEN GSDSFMHSMD PQLERQVETI RNLVDSYMAI VNKTVRDLMP KTIMHLMINN TKEFIFSELL ANLYSCGD Q NTLMEESAEQ AQRRDEMLRM YHALKEALSI IGNINTTTVS TPMPPPVDDS WLQVQSVPAG RRSPTSSPTP QRRAPAVPP ARPGSRGPAP GPPPAGSALG GAPPVPSRPG ASPDPFGPPP QVPSRPNRAP PGVPSRSGQA SPSRPESPRP PFDLGT

UniProtKB: Dynamin-1

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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.673 Å
Applied symmetry - Helical parameters - Δ&Phi: 26.155 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626859
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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