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- EMDB-49422: Cryo-EM structure of SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spi... -

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Entry
Database: EMDB / ID: EMD-49422
TitleCryo-EM structure of SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex
Map data
Sample
  • Complex: SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex
    • Protein or peptide: Piwi-like protein Siwi
    • RNA: piRNA
    • RNA: target RNA (39-nt)
    • Protein or peptide: GTSF1
    • Protein or peptide: Maelstrom
    • Protein or peptide: Spindle-E
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsSIWI / GTSF1 / Maelstrom / RNA BINDING PROTEIN / Spindle-E / 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 / regulatory ncRNA-mediated gene silencing / P granule ...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 / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / meiotic cell cycle / helicase activity / spermatogenesis / sequence-specific DNA binding / cell differentiation / RNA helicase / negative regulation of DNA-templated transcription / magnesium ion binding / RNA binding / ATP 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 / Tudor domain / HMG-box domain / Piwi domain profile. ...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 / Tudor domain / HMG-box domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / Helicase associated domain (HA2), ratchet-like / Tudor domain / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / PAZ domain profile. / PAZ domain / SNase-like, OB-fold superfamily / HMG boxes A and B DNA-binding domains profile. / High mobility group box domain / High mobility group box domain superfamily / Zinc finger C2H2 superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CHHC U11-48K-type domain-containing protein / Probable ATP-dependent RNA helicase spindle-E / HMG box domain-containing protein / Piwi-like protein Siwi
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSarkar S / Gebert LFR / MacRae IJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127090 United States
CitationJournal: Mol Cell / Year: 2025
Title: A conserved PIWI silencing complex detects piRNA-target engagement.
Authors: Dipayan De / Sucharita Sarkar / Luca F R Gebert / Timothy Wiryaman / Todd A Anzelon / Ian J MacRae /
Abstract: In animal germ cells, PIWI proteins use piRNAs to detect active selfish genetic elements. Base-pairing to a piRNA defines transposon recognition, but how this interaction triggers a defensive ...In animal germ cells, PIWI proteins use piRNAs to detect active selfish genetic elements. Base-pairing to a piRNA defines transposon recognition, but how this interaction triggers a defensive response remains unclear. Here, we identify a transposon recognition complex composed of the silkworm proteins Siwi, GTSF1, and Maelstrom. Biochemical and cryo-electron microscopy (cryo-EM) analyses show that extended piRNA-target pairing locks Siwi in a conformation that recruits GTSF1 and Maelstrom. Extended piRNA-target pairing is recognized by the N-terminal helix of Maelstrom and the first zinc finger of GTSF1, which act together to hold Siwi in an endonucleolytically active state. The resulting activated complex, termed Siwi, rapidly cleaves target RNAs and recruits the piRNA biogenesis factor Spindle-E. Structural predictions reveal related complexes in animals ranging from humans to sponges, indicating PIWI assembly is a conserved transposon recognition mechanism employed broadly across the metazoan kingdom.
History
DepositionFeb 25, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49422.png

Downloads & links

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Map

FileDownload / File: emd_49422.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.43017176 - 0.83418244
Average (Standard dev.)0.0001727753 (±0.03795725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49422_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49422_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex

EntireName: SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex
Components
  • Complex: SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex
    • Protein or peptide: Piwi-like protein Siwi
    • RNA: piRNA
    • RNA: target RNA (39-nt)
    • Protein or peptide: GTSF1
    • Protein or peptide: Maelstrom
    • Protein or peptide: Spindle-E
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex

SupramoleculeName: SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Bombyx mori (domestic silkworm)

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Macromolecule #1: Piwi-like protein Siwi

MacromoleculeName: Piwi-like protein Siwi / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 101.484242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEPRGRGRA RGRAGRGGDG GGPAPRRPGE QAGPSQQSMP PGPRPQPPSG WGPQSSVPPV RAGVPTPTAQ AGRASHRVTP TTHEHPGDI DVQQRMQKLE LGPHSSGGGD ASSVVGRGSR RGGGRVLPET ISILRTRPEA VTSKKGTSGT PLDLLANYFT V ETTPKWGL ...String:
MSEPRGRGRA RGRAGRGGDG GGPAPRRPGE QAGPSQQSMP PGPRPQPPSG WGPQSSVPPV RAGVPTPTAQ AGRASHRVTP TTHEHPGDI DVQQRMQKLE LGPHSSGGGD ASSVVGRGSR RGGGRVLPET ISILRTRPEA VTSKKGTSGT PLDLLANYFT V ETTPKWGL YQYHVDISPE EDSTGVRKAL MRVHSKTLGG YLFDGTVLYT VNRLHPDPME LYSDRKTDNE RMRILIKLTC EV SPGDYHY IQIFNIIIRK CFNLLKLQLM GRDYFDPEAK IDIPEFKLQI WPGYKTTINQ YEDRLLLVTE IAHKVLRMDT VLQ MLSEYA ATKGNNYKKI FLEDVVGKIV MTDYNKRTYR VDDVAWNVSP KSTFKMRDEN ITYIEYYYKK YNLRIQDPGQ PLLI SRSKP REIRAGLPEL IYLVPELCRQ TGLSDEMRAN FKLMRSLDVH TKIGPDKRIE KLNNFNRRFT STPEVVEELA TWSLK LSKE LVKIKGRQLP PENIIQANNV KYPAGDTTEG WTRDMRSKHL LAIAQLNSWV VITPERQRRD TESFIDLIIK TGGGVG FRM RSPDLVVIRH DGPIEYANMC EEVIARKNPA LILCVLARNY ADRYEAIKKK CTVDRAVPTQ VVCARNMSSK SAMSIAT KV AIQINCKLGG SPWTVDIPLP SLMVVGYDVC HDTRSKEKSF GAFVATLDKQ MTQYYSIVNA HTSGEELSSH MGFNIASA V KKFREKNGTY PARIFIYRDG VGDGQIPYVH SHEVAEIKKK LAEIYAGVEI KLAFIIVSKR INTRIFVQRG RSGENPRPG TVIDDVVTLP ERYDFYLVSQ NVREGTIAPT SYNVIEDTTG LNPDRIQRLT YKLTHLYFNC SSQVRVPSVC QYAHKLAFLA ANSLHNQPH YSLNETLYFL

UniProtKB: Piwi-like protein Siwi

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Macromolecule #4: GTSF1

MacromoleculeName: GTSF1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 17.358834 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEVTIANPKP NQMITCPYEK AHIVEHYRMH IHLQKCRKQH PACNKVQCPF DATHVVNDVE LDFHVTVCPK RHMLDTQLYI TDDEYRPTV EVHATPVLPS DENWDDETST SYIPDPSKKG AHIITKAKGL TRSERQSLRK ELIKTYRPLE

UniProtKB: CHHC U11-48K-type domain-containing protein

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Macromolecule #5: Maelstrom

MacromoleculeName: Maelstrom / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 49.900469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKKKTPQNP FFFFMMDYRK EQAEIGIKYA NTKELAEAAG PVWQNLRPTL KAKYEEKAKN EKEKNKQTGT KFTSTGIPIK VIEQQQREM KNAEDNEKKD IQNIVKLKVF DQSIKTEDFY VIDVNSYCKA NGDYLIGEFT VTQFSLQDGV KNSYHETIIP S CVPVGYMF ...String:
MPKKKTPQNP FFFFMMDYRK EQAEIGIKYA NTKELAEAAG PVWQNLRPTL KAKYEEKAKN EKEKNKQTGT KFTSTGIPIK VIEQQQREM KNAEDNEKKD IQNIVKLKVF DQSIKTEDFY VIDVNSYCKA NGDYLIGEFT VTQFSLQDGV KNSYHETIIP S CVPVGYMF DVKLGAEEFG LEMPGTDDAG PNYIQILANI IDYLKQKDRT VQVLPPMFTL PEKVDAVQNF ISQMCNCATE DD SLFRIYK LDTFFFTLIN AISSHHDEGF PKESLALTQL TKDLFDYTPG IACERHESLD RSNVCTTSRV KRWVFTILDR CCP LLGIPL QPGKHLPFDY DINGILIFKE ERKTRAAPSV PRTATASSNS SFINDSLNES FQSLNVTGET AASGSAPGRR VHKP LRMPR TDYSQRIQQA PELTEANFPT LTGHGRGRGL TRSNN

UniProtKB: HMG box domain-containing protein

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Macromolecule #6: Spindle-E

MacromoleculeName: Spindle-E / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 163.275547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDELKAFFNS PCPSSNQVTK LRGPLTGGFR IPKEDTMNDM NRKEAHRHMV VPSGTDYARE VKDRETELYL KNEIERKQYE SMSAGLESL EQLSLIGASV QNIGELNDEA MTEVYSKYSF QKKEDANNLA INSYKQQILD RIRGFPVVII EGPTGCGKTT Q VPQWLLDD ...String:
MDELKAFFNS PCPSSNQVTK LRGPLTGGFR IPKEDTMNDM NRKEAHRHMV VPSGTDYARE VKDRETELYL KNEIERKQYE SMSAGLESL EQLSLIGASV QNIGELNDEA MTEVYSKYSF QKKEDANNLA INSYKQQILD RIRGFPVVII EGPTGCGKTT Q VPQWLLDD CYHNRRPCKI IVTQPRRIAA ISITRRVAQE RGWDVGGLVG YQVGLDNRTS TDTRIHYVTT GVLLQKLVSA KT MNEYTHV ILDEVHERGQ EMDFLLLVVK KLLYTMSPAV KVVLMSATFN SKAFADYFMI PTPRGLQMST CIKVEKREHM FTV KTFYLN HLNKFGSVLQ NSMPKNGEPG INPEMHHLVI KLLNAFEQID KQEDNYMDRS EADLPSVLIF LPGINEIEDL YSSL TDHDL RTKVADLECA NYKWWVLPLH STITADEQVR VFQRAPLGHR KIILSTNIAE SSITVPDIKY VVDFCLMKVL EADAI TNFT SLKLCWASKT NCEQRAGRAG RVRDGRVYRL VTDKFYDSLR DECPPEIVRC PLERLALLAK MLDMGPPSDI LALAMD PPD MSNIHRTVLV LKEIGALKKT LDNEWSSSDG DLTYMGRIMA KLPIDVRASK LIVLGYVYGC LDECVIMAAA MSVKNVF NS PFRERLNAYN SKLTWADGST SDCIALLNVY KVWNHLRQQQ QFKQQGSEVQ WSRRFFVQVR ALRELDDMVR ELRLRLSR E GLESEGNASP WARNELPLAL KVIMAGAFYP QYFIQVSQDE EREREALRTL SGFDPRNTVY LRNFPDHQPG EVYASLIKK VVKQQIGDEP CVSFDKNGRK VFLTFNDGSY LSRSEKENSG DPTIPGQVAL PVYKCIKARQ LRLDIRIPLL PLEKANALAS AMQINNKDI SMERTVPRLP EIDDTHFPLK ITHEVNVGKF WVQYDDESTA AELRLIQYAL NHGPLLTHTG DVSADEIYAA P YADASGTV MCRVRVLKLL PMDMVEVAYM DYGGTGRVST CNLHALPAGA SRTCPPLGVP CALAGVAPAR RLHDRPAWSP QA YSCFREL ISRPRLIAKV YSVVHGVVAI ELLTDGGHVS VNEILIKKGF AVPCEESYES KLNHDLRQTA NELNLAQKRA YNK EQTEAA FYQLGDAAPP NYRECVADVC LKGPYSPLES SLHNLMYSSR DKPVQIDSSS VNSVLLDTEP QITYERLLVA AEVG QNESF SKLTLRLSTL MPNIPALPAI IALLFCPTAE LRRDSSATRY VSALCGLGAA PDAAPRFPEH DLLVNIDADL DVEDI GWIN HNRYLTDYML YCGEGQDMPT ADDEFRPQIP GIIRKNLMQL IKKRRKLRPT EAVPTAWEWK SVPEDELMEI TVPDMV ERA VLYELHVPLE LHPVSRDHLL ALKRDNDQLK LLVSRTPISS SAELSCKLCG TGPMPPHAMR LHLYSNIHKE KEEDFQM FQ T

UniProtKB: Probable ATP-dependent RNA helicase spindle-E

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Macromolecule #2: piRNA

MacromoleculeName: piRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.111833 KDa
SequenceString:
UGGAGUGUGA CAAUGGUGUU UGAU(A2M)

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Macromolecule #3: target RNA (39-nt)

MacromoleculeName: target RNA (39-nt) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.455611 KDa
SequenceString:
AAAAAAAUAU CAAACACCAU UGUCACACUC CAAAAAAAA

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1.11 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTRIStris(hydroxymethyl)aminomethane
100.0 mMNaClsodium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3412 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83871
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

5guh

chain_id: A, source_name: PDB, initial_model_type: experimental model
chain_id: E, source_name: AlphaFold, initial_model_type: in silico model
chain_id: F, source_name: AlphaFold, initial_model_type: in silico model
chain_id: G, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9nhs:
Cryo-EM structure of SIWI-piRNA-target(39-nt)-GTSF1-Maelstrom-Spindle-E complex

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