[English] 日本語
Yorodumi
- EMDB-40861: Cryo-EM of the GDP-bound human dynamin polymer assembled on the m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40861
TitleCryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state
Map dataGDP-bound human dynamin polymer assembled on the membrane in the super constricted state
Sample
  • Complex: GDP-bound human dynamin helical polymer assembled on the membrane
    • 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 / dynamin GTPase / chromaffin granule / regulation of vesicle size / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / Formation of annular gap junctions / endosome organization ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / Formation of annular gap junctions / endosome organization / Gap junction degradation / phosphatidylinositol-3,4,5-trisphosphate binding / Recycling pathway of L1 / EPH-ephrin mediated repulsion of cells / endocytic vesicle / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / receptor-mediated endocytosis / cell projection / protein homooligomerization / receptor internalization / endocytosis / GDP binding / presynapse / Clathrin-mediated endocytosis / protein homotetramerization / microtubule binding / microtubule / GTPase activity / synapse / protein kinase binding / GTP 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: 3.26 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
DepositionMay 24, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40861.png

Downloads & links

-
Map

FileDownload / File: emd_40861.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGDP-bound human dynamin polymer assembled on the membrane in the super constricted state
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: 0.0895
Minimum - Maximum-1.2789366 - 2.56036
Average (Standard dev.)0.004038495 (±0.044787973)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_40861_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 1

Fileemd_40861_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_40861_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GDP-bound human dynamin helical polymer assembled on the membrane

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

-
Supramolecule #1: GDP-bound human dynamin helical polymer assembled on the membrane

SupramoleculeName: GDP-bound human dynamin helical polymer assembled on the membrane
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.7 kDa/nm

-
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: 86.312625 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GPTGMGNRGM EDLIPLVNRL QDAFSAIGQN ADLDLPQIAV VGGQSAGASS VLENFVGRDF LPRGSGIVTR RPLVLQLVNA TTEYAEFLH CKGKKFTDFE EVRLEIEAET DRVTGTNKGI SPVPINLRVY SPHVLNLTLV DLPGMTKVPV GDQPPDIEFQ I RDMLMQFV ...String:
GPTGMGNRGM EDLIPLVNRL QDAFSAIGQN ADLDLPQIAV VGGQSAGASS VLENFVGRDF LPRGSGIVTR RPLVLQLVNA TTEYAEFLH CKGKKFTDFE EVRLEIEAET DRVTGTNKGI SPVPINLRVY SPHVLNLTLV DLPGMTKVPV GDQPPDIEFQ I RDMLMQFV TKENCLILAV SPANSDLANS DALKVAKEVD PQGQRTIGVI TKLDLMDEGT DARDVLENKL LPLRRGYIGV VN RSQKDID GKKDITAALA AERKFFLSHP SYRHLADRMG TPYLQKVLNQ QLTNHIRDTL PGLRNKLQSQ LLSIEKEVEE YKN FRPDDP ARKTKALLQM VQQFAVDFEK RIEGSGDQID TYELSGGARI NRIFHERFPF ELVKMEFDEK ELRREISYAI KNIH GIRTG LFTPDMAFET IVKKQVKKIR EPCLKCVDMV ISELISTVRQ CTKKLQQYPR LREEMERIVT THIREREGRT KEQVM LLID IELAYMNTNH EDFIGFANAQ QRSNQMNKKK TSGNQDEILV IRKGWLTINN IGIMKGGSKE YWFVLTAENL SWYKDD EEK EKKYMLSVDN LKLRDVEKGF MSSKHIFALF NTEQRNVYKD YRQLELACET QEEVDSWKAS FLRAGVYPER VGDKEKA SE TEENGSDSFM HSMDPQLERQ VETIRNLVDS YMAIVNKTVR DLMPKTIMHL MINNTKEFIF SELLANLYSC GDQNTLME E SAEQAQRRDE MLRMYHALKE ALSIIGNINT TTV

UniProtKB: Dynamin-1

-
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

-
Macromolecule #3: MAGNESIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.675 Å
Applied symmetry - Helical parameters - Δ&Phi: 26.146 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 609714
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more