[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

TitleAsymmetric dimeric assembly of Suv3 helicase facilitates processive RNA unwinding.
Journal, issue, pagesNat Commun, Year 2026
Publish dateApr 15, 2026
AuthorsMalay Patra / Monika Jain / Yi-Ching Li / Yi-Ping Chen / Bagher Golzarroshan / Hanna S Yuan /
PubMed AbstractHuman Suv3 is a dimeric helicase that collaborates with the exoribonuclease PNPase to mediate RNA decay and surveillance in mitochondria. Despite its pivotal role in maintaining mitochondrial ...Human Suv3 is a dimeric helicase that collaborates with the exoribonuclease PNPase to mediate RNA decay and surveillance in mitochondria. Despite its pivotal role in maintaining mitochondrial homeostasis, the molecular mechanism underlying Suv3-mediated RNA unwinding has remained elusive. Here, we present near-atomic-resolution cryogenic electron microscopy structures of Suv3 captured in four functional states: the apo form, two binary complexes with ADP and single-stranded RNA (ssRNA), and a ternary complex with ssRNA and an ATP analog (AMP-PNP). These structures reveal an unexpected asymmetric dimeric organization, in which only one of the two protomers engages in the initial binding of ADP, ssRNA, or both ssRNA and AMP-PNP. Complementary biochemical analyses demonstrate that Suv3 dimerization significantly enhances RNA-binding and unwinding efficiency in an ATP-hydrolysis-dependent manner. Together, these findings provide key insights into the dimeric architecture of Suv3 and establish a mechanistic framework for its coordinated function in processive RNA unwinding.
External linksNat Commun / PubMed:41986356
MethodsEM (single particle)
Resolution3.47 - 4.42 Å
Structure data

64948

9vc8

EMDB-64948: Cryo-EM map of Suv3 monomer
PDB-9vc8: Cryo-EM structure of Suv3 monomer
Method: EM (single particle) / Resolution: 4.04 Å

64952

9vcc

EMDB-64952: Cryo-EM map of Suv3 dimer
PDB-9vcc: Cryo-EM structure of Suv3 dimer
Method: EM (single particle) / Resolution: 3.92 Å

64967

9vct

EMDB-64967, PDB-9vct:
Cryo-EM structure of monomeric Suv3-ADP complex
Method: EM (single particle) / Resolution: 3.47 Å

64968

9vcu

EMDB-64968, PDB-9vcu:
Cryo-EM structure of dimeric Suv3-ADP complex
Method: EM (single particle) / Resolution: 3.84 Å

64969

9vcv

EMDB-64969, PDB-9vcv:
Cryo-EM structure of monomeric Suv3-ssRNA complex
Method: EM (single particle) / Resolution: 3.63 Å

64970

9vcw

EMDB-64970: Cryo-EM map of dimeric Suv3-ssRNA complex
PDB-9vcw: Cryo-EM structure of dimeric Suv3-ssRNA complex
Method: EM (single particle) / Resolution: 3.75 Å

64972

9vd0

EMDB-64972: Cryo-EM map of monomeric Suv3-ssRNA-AMPPNP complex
PDB-9vd0: Cryo-EM structure of monomeric Suv3-ssRNA-AMPPNP complex
Method: EM (single particle) / Resolution: 4.42 Å

64973

9vd1

EMDB-64973, PDB-9vd1:
Cryo-EM structure of Dimeric Suv3-ssRNA-AMPPNP complex
Method: EM (single particle) / Resolution: 4.16 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsHYDROLASE / Helicase / RNA binding protein / Suv3 dimer / dimeric Suv3-ADP complex / HYDROLASE/RNA / HYDROLASE-RNA complex

+
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