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- PDB-9nhc: Cryo-EM structure of SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex -

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Basic information

Entry
Database: PDB / ID: 9nhc
TitleCryo-EM structure of SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
Components
  • GTSF1
  • Maelstrom
  • Piwi-like protein Siwi
  • piRNA
  • target RNA (49-nt)
KeywordsRNA BINDING PROTEIN/RNA / SIWI / GTSF1 / Maelstrom / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


female sex determination / regulation of miRNA-mediated gene silencing / PET complex / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / piRNA processing / male meiotic nuclear division / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters ...female sex determination / regulation of miRNA-mediated gene silencing / PET complex / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / piRNA processing / male meiotic nuclear division / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / meiotic cell cycle / spermatogenesis / sequence-specific DNA binding / cell differentiation / negative regulation of DNA-templated transcription / magnesium ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Maelstrom domain / Protein maelstrom / piRNA pathway germ-plasm component / TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / U11-48K-like CHHC zinc finger / Zinc finger CHHC U11-48K-type profile. / Piwi, N-terminal domain / HMG-box domain / Piwi domain profile. / Piwi domain ...Maelstrom domain / Protein maelstrom / piRNA pathway germ-plasm component / TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / U11-48K-like CHHC zinc finger / Zinc finger CHHC U11-48K-type profile. / Piwi, N-terminal domain / HMG-box domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / HMG boxes A and B DNA-binding domains profile. / High mobility group box domain / High mobility group box domain superfamily / Zinc finger C2H2 superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / CHHC U11-48K-type domain-containing protein / HMG box domain-containing protein / Piwi-like protein Siwi
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSarkar, S. / Gebert, L.F.R. / MacRae, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127090 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
Authors: Sarkar, S. / Gebert, L.F.R. / MacRae, I.J.
History
DepositionFeb 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Piwi-like protein Siwi
B: piRNA
C: target RNA (49-nt)
E: GTSF1
F: Maelstrom
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,70410
Polymers192,4595
Non-polymers2455
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules AEF

#1: Protein Piwi-like protein Siwi


Mass: 101484.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: Siwi / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A8D8P8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#4: Protein GTSF1


Mass: 17358.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8R1WGS4
#5: Protein Maelstrom


Mass: 49900.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8R2M2N1

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain piRNA


Mass: 8111.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain target RNA (49-nt)


Mass: 15603.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 5 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTRIS1
2100 mMsodium chlorideNaCl1
30.5 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 0.86 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 5281

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Processing

EM software
IDNameVersionCategory
7UCSF ChimeraX1.8model fitting
9PHENIX1.20.1model refinement
10Coot0.9.8.1model refinement
11UCSF ChimeraX1.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198296 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDSource nameType
15GUH

5guh

A5GUHAPDBexperimental model
2EAlphaFoldin silico model
3FAlphaFoldin silico model

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