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- EMDB-49408: Cryo-EM structure of SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49408
TitleCryo-EM structure of SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
Map data
Sample
  • Complex: SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
    • Protein or peptide: Piwi-like protein Siwi
    • RNA: piRNA
    • RNA: target RNA (49-nt)
    • Protein or peptide: GTSF1
    • Protein or peptide: Maelstrom
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsSIWI / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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: To Be Published
Title: Cryo-EM structure of SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
Authors: Sarkar S / Gebert LFR / MacRae IJ
History
DepositionFeb 24, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49408.png

Downloads & links

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Map

FileDownload / File: emd_49408.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.1489258 - 3.2139947
Average (Standard dev.)0.00013729112 (±0.08007659)
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_49408_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49408_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex

EntireName: SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
Components
  • Complex: SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex
    • Protein or peptide: Piwi-like protein Siwi
    • RNA: piRNA
    • RNA: target RNA (49-nt)
    • Protein or peptide: GTSF1
    • Protein or peptide: Maelstrom
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex

SupramoleculeName: SIWI-piRNA-target(49-nt)-GTSF1-Maelstrom complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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 #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 (49-nt)

MacromoleculeName: target RNA (49-nt) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.603524 KDa
SequenceString:
AAAAAAAUAU CAAACACCAU UGUCACACUC CAAAAAAAAC CCCAAAACC

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / 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

Concentration0.86 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: 5281 / 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198296
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
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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