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- EMDB-11932: CryoEM structure of the super-constricted two-start dynamin 1 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-11932
TitleCryoEM structure of the super-constricted two-start dynamin 1 filament
Map data
Sample
  • Complex: dynamin 1
    • Protein or peptide: Dynamin-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
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: 3.74 Å
AuthorsLiu JW / Zhang PJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: CryoEM structure of the super-constricted two-start dynamin 1 filament.
Authors: Jiwei Liu / Frances Joan D Alvarez / Daniel K Clare / Jeffrey K Noel / Peijun Zhang /
Abstract: Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical ...Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical collar and to constrict the underlying membrane. Two helical forms were observed: the one-start helix in the constricted state and the two-start helix in the super-constricted state. Here we report the cryoEM structure of a super-constricted two-start dynamin 1 filament at 3.74 Å resolution. The two strands are joined by the conserved GTPase dimeric interface. In comparison with the one-start structure, a rotation around Hinge 1 is observed, essential for communicating the chemical power of the GTPase domain and the mechanical force of the Stalk and PH domain onto the underlying membrane. The Stalk interfaces are well conserved and serve as fulcrums for adapting to changing curvatures. Relative to one-start, small rotations per interface accumulate to bring a drastic change in the helical pitch. Elasticity theory rationalizes the diversity of dynamin helical symmetries and suggests corresponding functional significance.
History
DepositionNov 9, 2020-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateNov 10, 2021-
Current statusNov 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ax3
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ax3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11932.png

Downloads & links

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Map

FileDownload / File: emd_11932.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 510 pix.
= 534.48 Å		1.05 Å/pix.
x 510 pix.
= 534.48 Å		1.05 Å/pix.
x 510 pix.
= 534.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0115 / Movie #1: 0.0115
Minimum - Maximum-0.030506417 - 0.07733267
Average (Standard dev.)0.0002863064 (±0.0023186973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 534.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z534.480534.480534.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-0.0310.0770.000

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Supplemental data

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Sample components

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Entire : dynamin 1

EntireName: dynamin 1
Components
  • Complex: dynamin 1
    • Protein or peptide: Dynamin-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: dynamin 1

SupramoleculeName: dynamin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Dynamin-1

MacromoleculeName: Dynamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.536359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGKSSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTEY AEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP PDIEFQIRDM L MQFVTKEN ...String:
MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGKSSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTEY AEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP PDIEFQIRDM L MQFVTKEN CLILAVSPAN SDLANSDALK VAKEVDPQGQ RTIGVITKLD LMDEGTDARD VLENKLLPLR RGYIGVVNRS QK DIDGKKD ITAALAAERK FFLSHPSYRH LADRMGTPYL QKVLNQQLTN HIRDTLPGLR NKLQSQLLSI EKEVEEYKNF RPD DPARKT KALLQMVQQF AVDFEKRIEG SGDQIDTYEL SGGARINRIF HERFPFELVK MEFDEKELRR EISYAIKNIH GIRT GLFTP DMAFETIVKK QVKKIREPCL KCVDMVISEL ISTVRQCTKK LQQYPRLREE MERIVTTHIR EREGRTKEQV MLLID IELA YMNTNHEDFI GFANAQQRSN QMNKKKTSGN QDEILVIRKG WLTINNIGIM KGGSKEYWFV LTAENLSWYK DDEEKE KKY MLSVDNLKLR DVEKGFMSSK HIFALFNTEQ RNVYKDYRQL ELACETQEEV DSWKASFLRA GVYPERVGDK EKASETE EN GSDSFMHSMD PQLERQVETI RNLVDSYMAI VNKTVRDLMP KTIMHLMINN TKEFIFSELL ANLYSCGDQN TLMEESAE Q AQRRDEMLRM YHALKEALSI IGNINTTTVS TPMPPPVDDS WLQVQSVPAG RRSPTSSPTP QRRAPAVPPA RPGSRGPAP GPPPAGSALG GAPPVPSRPG ASPDPFGPPP QVPSRPNRAP PGVPSRSGQA SPSRPESPRP PFDL

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Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 36 / Formula: GCP
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 36 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 13.58 Å
Applied symmetry - Helical parameters - Δ&Phi: 24.43 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16772
Final angle assignmentType: NOT APPLICABLE

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