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- EMDB-64969: Cryo-EM structure of monomeric Suv3-ssRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64969
TitleCryo-EM structure of monomeric Suv3-ssRNA complex
Map dataMonomeric Suv3-ssRNA complex.
Sample
  • Complex: Monomeric Suv3-ssRNA complex.
    • Protein or peptide: ATP-dependent RNA helicase SUPV3L1, mitochondrial
    • RNA: RNA (5'-R(P*UP*UP*UP*U)-3')
KeywordsHelicase / RNA binding protein / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


mitochondrial ncRNA surveillance / mitochondrial mRNA surveillance / mitochondrial RNA surveillance / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / Mitochondrial RNA degradation / mitochondrial RNA catabolic process / 3'-5' RNA helicase activity ...mitochondrial ncRNA surveillance / mitochondrial mRNA surveillance / mitochondrial RNA surveillance / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / Mitochondrial RNA degradation / mitochondrial RNA catabolic process / 3'-5' RNA helicase activity / RNA catabolic process / mitochondrial nucleoid / DNA helicase activity / helicase activity / mitochondrion organization / double-stranded RNA binding / positive regulation of cell growth / DNA recombination / RNA helicase activity / RNA helicase / mitochondrial matrix / negative regulation of apoptotic process / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Suv3, C-terminal domain 1 / Suv3, N-terminal / : / Suv3 helical N-terminal domain / Suv3 C-terminal domain 1 / Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Suv3, DEXQ-box helicase domain / ATP-dependent RNA helicase SUV3 C-terminal domain / DEXQ-box helicase domain of Suv3 / : ...Suv3, C-terminal domain 1 / Suv3, N-terminal / : / Suv3 helical N-terminal domain / Suv3 C-terminal domain 1 / Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Suv3, DEXQ-box helicase domain / ATP-dependent RNA helicase SUV3 C-terminal domain / DEXQ-box helicase domain of Suv3 / : / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase, C-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase SUPV3L1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsPatra M / Yuan HS
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-110-L02 Taiwan
CitationJournal: Nat Commun / Year: 2026
Title: Asymmetric dimeric assembly of Suv3 helicase facilitates processive RNA unwinding.
Authors: Malay Patra / Monika Jain / Yi-Ching Li / Yi-Ping Chen / Bagher Golzarroshan / Hanna S Yuan /
Abstract: 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 ...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.
History
DepositionJun 6, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64969.png

Downloads & links

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Map

FileDownload / File: emd_64969.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomeric Suv3-ssRNA complex.
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.92449445 - 1.5425735
Average (Standard dev.)0.0005332317 (±0.0324744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64969_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_64969_half_map_2.map
Projections & Slices
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Sample components

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Entire : Monomeric Suv3-ssRNA complex.

EntireName: Monomeric Suv3-ssRNA complex.
Components
  • Complex: Monomeric Suv3-ssRNA complex.
    • Protein or peptide: ATP-dependent RNA helicase SUPV3L1, mitochondrial
    • RNA: RNA (5'-R(P*UP*UP*UP*U)-3')

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Supramolecule #1: Monomeric Suv3-ssRNA complex.

SupramoleculeName: Monomeric Suv3-ssRNA complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP-dependent RNA helicase SUPV3L1, mitochondrial

MacromoleculeName: ATP-dependent RNA helicase SUPV3L1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.450875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASSSASGGS KIPNTSLFVP LTVKPQGPSA DGDVGAELTR PLDKNEVKKV LDKFYKRKEI QKLGADYGL DARLFHQAFI SFRNYIMQSH SLDVDIHIVL NDICFGAAHA DDLFPFFLRH AKQIFPVLDC KDDLRKISDL R IPPNWYPD ...String:
MGSSHHHHHH SSGLVPRGSH MASSSASGGS KIPNTSLFVP LTVKPQGPSA DGDVGAELTR PLDKNEVKKV LDKFYKRKEI QKLGADYGL DARLFHQAFI SFRNYIMQSH SLDVDIHIVL NDICFGAAHA DDLFPFFLRH AKQIFPVLDC KDDLRKISDL R IPPNWYPD ARAMQRKIIF HSGPTNSGKT YHAIQKYFSA KSGVYCGPLK LLAHEIFEKS NAAGVPCDLV TGEERVTVQP NG KQASHVS CTVEMCSVTT PYEVAVIDEI QMIRDPARGW AWTRALLGLC AEEVHLCGEP AAIDLVMELM YTTGEEVEVR DYK RLTPIS VLDHALESLD NLRPGDCIVC FSKNDIYSVS RQIEIRGLES AVIYGSLPPG TKLAQAKKFN DPNDPCKILV ATDA IGMGL NLSIRRIIFY SLIKPSINEK GERELEPITT SQALQIAGRA GRFSSRFKEG EVTTMNHEDL SLLKEILKRP VDPIR AAGL HPTAEQIEMF AYHLPDATLS NLIDIFVDFS QVDGQYFVCN MDDFKFSAEL IQHIPLSLRV RYVFCTAPIN KKQPFV CSS LLQFARQYSR NEPLTFAWLR RYIKWPLLPP KNIKDLMDLE AVHDVLDLYL WLSYRFMDMF PDASLIRDLQ KELDGII QD GVHNITKLIK MSETHKLLNL EGFPSGSQSR LSGTLKSQAR RTRGTKALGS KATEPPSPDA GELSLASRLV QQGLLTPD M LKQLEKEWMT QQTEHNKEKT ESGTHPKGTR RKKKEPDSD

UniProtKB: ATP-dependent RNA helicase SUPV3L1, mitochondrial

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.179706 KDa
SequenceString:
UUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8 / Details: 20mM HEPES pH=8.0, 300 mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140359
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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