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- EMDB-7957: Cryo-EM of the GMPPCP-bound human dynamin-1 polymer assembled on ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7957
TitleCryo-EM of the GMPPCP-bound human dynamin-1 polymer assembled on the membrane in the constricted state
Map dataGMPPCP-bound human dynamin-1
Sample
  • Complex: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer tube
    • 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: 3.75 Å
AuthorsKong L / Wang H / Fang S / Canagarajah B / Kehr AD / Rice WJ / Hinshaw JE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 486 OD019994-01 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM of the dynamin polymer assembled on lipid membrane.
Authors: Leopold Kong / Kem A Sochacki / Huaibin Wang / Shunming Fang / Bertram Canagarajah / Andrew D Kehr / William J Rice / Marie-Paule Strub / Justin W Taraska / Jenny E Hinshaw /
Abstract: Membrane fission is a fundamental process in the regulation and remodelling of cell membranes. Dynamin, a large GTPase, mediates membrane fission by assembling around, constricting and cleaving the ...Membrane fission is a fundamental process in the regulation and remodelling of cell membranes. Dynamin, a large GTPase, mediates membrane fission by assembling around, constricting and cleaving the necks of budding vesicles. Here we report a 3.75 Å resolution cryo-electron microscopy structure of the membrane-associated helical polymer of human dynamin-1 in the GMPPCP-bound state. The structure defines the helical symmetry of the dynamin polymer and the positions of its oligomeric interfaces, which were validated by cell-based endocytosis assays. Compared to the lipid-free tetramer form, membrane-associated dynamin binds to the lipid bilayer with its pleckstrin homology domain (PHD) and self-assembles across the helical rungs via its guanine nucleotide-binding (GTPase) domain. Notably, interaction with the membrane and helical assembly are accommodated by a severely bent bundle signalling element (BSE), which connects the GTPase domain to the rest of the protein. The BSE conformation is asymmetric across the inter-rung GTPase interface, and is unique compared to all known nucleotide-bound states of dynamin. The structure suggests that the BSE bends as a result of forces generated from the GTPase dimer interaction that are transferred across the stalk to the PHD and lipid membrane. Mutations that disrupted the BSE kink impaired endocytosis. We also report a 10.1 Å resolution cryo-electron microscopy map of a super-constricted dynamin polymer showing localized conformational changes at the BSE and GTPase domains, induced by GTP hydrolysis, that drive membrane constriction. Together, our results provide a structural basis for the mechanism of action of dynamin on the lipid membrane.
History
DepositionJun 2, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseAug 1, 2018-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0412
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0412
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dlu
  • Surface level: 0.0412
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6dlu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7957.png

Downloads & links

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Map

FileDownload / File: emd_7957.map.gz / Format: CCP4 / Size: 691.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGMPPCP-bound human dynamin-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 566 pix.
= 605.62 Å		1.07 Å/pix.
x 566 pix.
= 605.62 Å		1.07 Å/pix.
x 566 pix.
= 605.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04122 / Movie #1: 0.0412
Minimum - Maximum-0.073226474 - 0.1969174
Average (Standard dev.)0.0007914406 (±0.006119845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin111
Dimensions566566566
Spacing566566566
CellA=B=C: 605.62006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z566566566
origin x/y/z0.0000.0000.000
length x/y/z605.620605.620605.620
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS566566566
D min/max/mean-0.0730.1970.001

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Supplemental data

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Sample components

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Entire : GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphati...

EntireName: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer tube
Components
  • Complex: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer tube
    • Protein or peptide: Dynamin-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphati...

SupramoleculeName: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer tube
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightExperimental: 98 kDa/nm

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Macromolecule #1: Dynamin-1

MacromoleculeName: Dynamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.859148 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 IGDINTT

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Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / 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: 2 / 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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 67.0 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: 6.35 Å
Applied symmetry - Helical parameters - Δ&Phi: 23.68 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.6) / Number images used: 452959
Startup modelType of model: NONE / Details: featureless cylinder used
Final angle assignmentType: NOT APPLICABLE

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