[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleCryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.
Journal, issue, pagesDev Cell, Vol. 59, Issue 14, Page 1783-11793.e5, Year 2024
Publish dateJul 22, 2024
AuthorsJohn 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 /
PubMed AbstractDynamin 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.
External linksDev Cell / PubMed:38663399 / PubMed Central
MethodsEM (helical sym.)
Resolution2.84 - 3.97 Å
Structure data

EMDB-40861, PDB-8sxz:
Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state
PDB-8tyn: Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state (tetramer model)
Method: EM (helical sym.) / Resolution: 3.26 Å

EMDB-40901, PDB-8sz4:
Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state showing the PH domain
Method: EM (helical sym.) / Resolution: 2.86 Å

EMDB-40902, PDB-8sz7:
Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state showing the second PH domain
Method: EM (helical sym.) / Resolution: 2.84 Å

EMDB-40903, PDB-8sz8:
Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state (full helix)
Method: EM (helical sym.) / Resolution: 3.55 Å

EMDB-40942, PDB-8t0k, PDB-8tym:
Cryo-EM of the GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state
Method: EM (helical sym.) / Resolution: 3.58 Å

EMDB-40946, PDB-8t0r:
Cryo-EM of the GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix)
Method: EM (helical sym.) / Resolution: 3.97 Å

Chemicals

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

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsHYDROLASE / dynamin / membrane / fission / lipid / tubule / scission / endocytosis

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more