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- PDB-9vd0: Cryo-EM structure of monomeric Suv3-ssRNA-AMPPNP complex -

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Basic information

Entry
Database: PDB / ID: 9vd0
TitleCryo-EM structure of monomeric Suv3-ssRNA-AMPPNP complex
Components
  • ATP-dependent RNA helicase SUPV3L1, mitochondrial
  • RNA (5'-R(P*UP*U)-3')
KeywordsHYDROLASE/RNA / Helicase / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / ATP-dependent RNA helicase SUPV3L1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å
AuthorsPatra, M. / Yuan, H.S.
Funding support Taiwan, 1items
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 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: RNA (5'-R(P*UP*U)-3')
A: ATP-dependent RNA helicase SUPV3L1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5243
Polymers86,0182
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (5'-R(P*UP*U)-3')


Mass: 567.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein ATP-dependent RNA helicase SUPV3L1, mitochondrial / Suppressor of var1 3-like protein 1 / SUV3-like protein 1


Mass: 85450.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPV3L1, SUV3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYB8, RNA helicase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Suv3-ssRNA-AMPPNP / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 20 mM HEPES pH=8.0, 300 mM Nacl
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79467 / Symmetry type: POINT
RefinementHighest resolution: 4.42 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035015
ELECTRON MICROSCOPYf_angle_d0.6246805
ELECTRON MICROSCOPYf_dihedral_angle_d9.722680
ELECTRON MICROSCOPYf_chiral_restr0.042760
ELECTRON MICROSCOPYf_plane_restr0.005864

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