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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: 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
SampleGMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer tube:
Dynamin-1 / (ligand) x 2
Function / homologyDynamin, GTPase domain / Dynamin central region / Pleckstrin homology domain / Dynamin GTPase effector / PH-like domain superfamily / Dynamin, GTPase region, conserved site / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Dynamin-1 ...Dynamin, GTPase domain / Dynamin central region / Pleckstrin homology domain / Dynamin GTPase effector / PH-like domain superfamily / Dynamin, GTPase region, conserved site / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Dynamin-1 / Dynamin-type guanine nucleotide-binding (G) domain / PH domain / Dynamin family / Dynamin GTPase effector domain / Dynamin central domain / Dynamin-type guanine nucleotide-binding (G) domain signature. / PH domain profile. / GED domain profile. / Dynamin-type guanine nucleotide-binding (G) domain profile. / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Gap junction degradation / Formation of annular gap junctions / MHC class II antigen presentation / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / Clathrin-mediated endocytosis / synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / synaptic transmission, GABAergic / dynamin family protein polymerization involved in mitochondrial fission / D2 dopamine receptor binding / varicosity / membrane coat / G protein-coupled receptor internalization / positive regulation of synaptic vesicle endocytosis / clathrin-dependent endocytosis / endosome organization / mitochondrial fission / response to amyloid-beta / membrane fusion / toxin transport / nitric-oxide synthase binding / mitochondrial membrane / adult locomotory behavior / photoreceptor inner segment / synaptic vesicle / sensory perception of sound / ephrin receptor signaling pathway / protein tetramerization / SH3 domain binding / endocytosis / receptor-mediated endocytosis / microtubule binding / microtubule / protein C-terminus binding / protein-containing complex binding / protein dimerization activity / GTPase activity / myelin sheath / GTP binding / protein kinase binding / Golgi apparatus / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / nucleus / Dynamin-1
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.75 Å resolution
AuthorsKong L / Wang H / Fang S / Canagarajah B / Kehr AD / Rice WJ / Hinshaw JE
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
Validation ReportPDB-ID: 6dlu

SummaryFull reportAbout validation report
DateDeposition: Jun 2, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Aug 1, 2018 / Last update: Aug 1, 2018

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Structure visualization

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

Downloads & links

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Map

Fileemd_7957.map.gz (map file in CCP4 format, 725287 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
566 pix
1.07 Å/pix.
= 605.62 Å
566 pix
1.07 Å/pix.
= 605.62 Å
566 pix
1.07 Å/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
Contour Level:0.04122 (by author), 0.0412 (movie #1):
Minimum - Maximum-0.073226474 - 0.1969174
Average (Standard dev.)0.0007914406 (0.006119845)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions566566566
Origin1.1.1.
Limit566.566.566.
Spacing566566566
CellA=B=C: 605.62006 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 4

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Component #1: protein, GMPPCP-bound Human Dynamin-1 helical polymer encasing a ...

ProteinName: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer tube
Recombinant expression: No
MassExperimental: 98 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Dynamin-1

ProteinName: Dynamin-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 85.859148 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: ligand, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

LigandName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.521208 kDa

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED / Delta z: 6.35 Å / Delta phi: 23.68 deg.
Sample solutionpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 67 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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