[English] 日本語
Yorodumi
- EMDB-48697: Cryo-EM structure of ancestral Dicer helicase bound to 27-bp dsRN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48697
TitleCryo-EM structure of ancestral Dicer helicase bound to 27-bp dsRNA in post-hydrolysis closed state
Map data
Sample
  • Complex: Ancestral metazoan Dicer helicase in complex 27-bp blunt dsRNA and ATP
    • Protein or peptide: AncD1D2
    • RNA: RNA (27-MER)
    • RNA: RNA (27-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsRNA helicase / dsRBM / ANTIVIRAL PROTEIN-RNA complex
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAderounmu AM / Consalvo CD / Shen PS / Bass BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM141262 United States
CitationJournal: bioRxiv / Year: 2025
Title: Biochemical and structural basis of Dicer helicase function unveiled by resurrecting ancient proteins.
Authors: Adedeji M Aderounmu / Josephine Maus-Conn / Claudia D Consalvo / Peter S Shen / Brenda L Bass /
Abstract: A fully functional Dicer helicase, present in the modern arthropod, uses energy generated during ATP hydrolysis to power translocation on bound dsRNA, enabling the processive dsRNA cleavage required ...A fully functional Dicer helicase, present in the modern arthropod, uses energy generated during ATP hydrolysis to power translocation on bound dsRNA, enabling the processive dsRNA cleavage required for efficient antiviral defense. However, modern Dicer orthologs exhibit divergent helicase functions that affect their ability to contribute to antiviral defense, and moreover, mechanisms that couple ATP hydrolysis to Dicer helicase movement on dsRNA remain enigmatic. Here, we used biochemical and structural analyses of ancestrally reconstructed Dicer helicases to map evolution of dsRNA binding affinity, ATP hydrolysis and translocation. We found that loss of affinity for dsRNA occurred early in Dicer evolution, coinciding with a decline in translocation activity, despite preservation of ATP hydrolysis activity, exemplified by the ancient deuterostome Dicer. Ancestral nematode Dicer also exhibited significant decline in ATP hydrolysis and translocation, but studies of antiviral activities in the modern nematode indicate Dicer retained a role in antiviral defense by recruiting a second helicase. Cryo-EM analyses of an ancient metazoan Dicer allowed capture of multiple helicase states revealing the mechanism that connects each step of ATP hydrolysis to unidirectional movement along dsRNA. Overall, our study rationalizes the diversity in modern Dicer helicases by connecting ancestral functions to observations in extant enzymes.
History
DepositionJan 17, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48697.png

Downloads & links

-
Map

FileDownload / File: emd_48697.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 279.04 Å		0.87 Å/pix.
x 320 pix.
= 279.04 Å		0.87 Å/pix.
x 320 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.872 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.2241419 - 0.45199507
Average (Standard dev.)-0.00020066233 (±0.0087782955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 279.03998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_48697_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_48697_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ancestral metazoan Dicer helicase in complex 27-bp blunt dsRNA and ATP

EntireName: Ancestral metazoan Dicer helicase in complex 27-bp blunt dsRNA and ATP
Components
  • Complex: Ancestral metazoan Dicer helicase in complex 27-bp blunt dsRNA and ATP
    • Protein or peptide: AncD1D2
    • RNA: RNA (27-MER)
    • RNA: RNA (27-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: Ancestral metazoan Dicer helicase in complex 27-bp blunt dsRNA and ATP

SupramoleculeName: Ancestral metazoan Dicer helicase in complex 27-bp blunt dsRNA and ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 93 KDa

-
Macromolecule #1: AncD1D2

MacromoleculeName: AncD1D2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 75.480609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDETDEDEFT PRPYQVELLE RAMKKNTIVC LGTGSGKTFI AVMLIKELAH EIRGPFNEGG KRTFFLVNTV PLVNQQAKVI RKHTSLKVG EYVGDMGVDS WNKEKWNQEF EKHQVLVMTA QIFLDILNHG FISLSQVNLL IFDECHHAVK NHPYRQIMRH Y KNLEQNDR ...String:
MDETDEDEFT PRPYQVELLE RAMKKNTIVC LGTGSGKTFI AVMLIKELAH EIRGPFNEGG KRTFFLVNTV PLVNQQAKVI RKHTSLKVG EYVGDMGVDS WNKEKWNQEF EKHQVLVMTA QIFLDILNHG FISLSQVNLL IFDECHHAVK NHPYRQIMRH Y KNLEQNDR PRILGLTASV INSKCKPNQV EKKIKELEAT LNSRVVTASD LEEVAVQKYA TKPKEIIVSY NSDRKSDTSE VI ENIINQA LEQLSNIEET SNLNDTNSLK QIKKVLRDIK NILDELGPWC AHRVIKSRIR QLEKRESETA EELRTIRELL QSI FEQIIN VLKNLEKLQK NNSVEFVSPK VKKLLEILKQ YFSNNNNSSK ELCGIIFVER RYTAYVLYKL LNELSAKRDD DFSF IKCDF VVGHNSSPSS KEKSTEMNSK KQKEVLKKFR KGECNLLVAT SVVEEGIDIP KCNLVVRFDL PKNFRSYVQS KGRAR AKNS KYIIMVEEDE KNKFQEDLNQ YQEIEKILLR LCHNRDAPSE EDFDSFEDEL LPPYMPYGTD GPRVTMSSAI SLLHRY CSK LPSDRFTTLT PKFTYIEQNN EEENKMFRCT LRLPINSPLR EPITGQPMPS KKLAKRSAAL EACKKLHEMG ELDDHLL PV KISRKNAELK

-
Macromolecule #2: RNA (27-MER)

MacromoleculeName: RNA (27-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.572096 KDa
SequenceString:
AUACGUCCUG AUAGUUAGUA UCCAUCG

-
Macromolecule #3: RNA (27-MER)

MacromoleculeName: RNA (27-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.658198 KDa
SequenceString:
CGAUGGAUAC UAACUAUCAG GACGUAU

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 100 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold 2 model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 315941
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9mw8:
Cryo-EM structure of ancestral Dicer helicase bound to 27-bp dsRNA in post-hydrolysis closed state

+
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