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- PDB-9s1e: Cryo-EM structure of the endogeneous MIWI in complex with pachyte... -

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Basic information

Entry
Database: PDB / ID: 9s1e
TitleCryo-EM structure of the endogeneous MIWI in complex with pachytene piRNA at 2.8A
Components
  • Piwi-like protein 1
  • RNA (5'-R(P*UP*UP*AP*CP*C)-3')
KeywordsRNA BINDING PROTEIN / MIWI / PIWIL1 / piRNA / slicer / pachytene piRNA
Function / homology
Function and homology information


primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / regulation of cytoplasmic translation / transposable element silencing by piRNA-mediated heterochromatin formation / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / regulation of cytoplasmic translation / transposable element silencing by piRNA-mediated heterochromatin formation / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / spermatid development / RNA endonuclease activity / meiotic cell cycle / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi ...GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / Piwi-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsRaad, N.G. / Fernandez-Rodriguez, C. / Pandey, R.R. / Mohammed, I. / Uchikawa, E. / Burger, F. / Homolka, D. / Pillai, R.S.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_215346 Switzerland
Swiss National Science Foundation#51NF40-205601 Switzerland
Other privateThe Lalor Foundation
CitationJournal: Cell Rep / Year: 2026
Title: Structure of the MIWI endoribonuclease bound to pachytene piRNAs from mouse testes.
Authors: Nicole Raad / Carmen Fernandez-Rodriguez / Radha Raman Pandey / Inayathulla Mohammed / Emiko Uchikawa / Fabienne Burger / David Homolka / Ramesh S Pillai /
Abstract: PIWI-interacting RNAs (piRNAs) guide PIWI endoribonucleases to destroy transposon transcripts, ensuring animal fertility. Here, we report the cryo-electron microscopy structure of the MIWI-pachytene ...PIWI-interacting RNAs (piRNAs) guide PIWI endoribonucleases to destroy transposon transcripts, ensuring animal fertility. Here, we report the cryo-electron microscopy structure of the MIWI-pachytene piRNA complex isolated from mouse testes. The piRNA is held via non-specific charge-based interactions with the RNA backbone and by specific recognition of the first nucleotide uridine by residues within the MID and PIWI domains. The first six nucleotides of the guide RNA take up the A-form conformation to facilitate pairing with the target. The RNA channel is wider than that observed in insect PIWI proteins, explaining the tolerance for piRNA seed:target mismatches. The PIWI endonuclease domain is in an inactive "un-plugged" state, with the loop containing a catalytic residue (E671) requiring structural re-orientation for activity. Furthermore, the PIWI domain reveals a conserved pre-formed pocket that may serve to accommodate a conserved tryptophan from the interacting factor GTSF1 to promote small RNA-guided endoribonuclease activity.
History
DepositionJul 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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*UP*AP*CP*C)-3')
B: Piwi-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2823
Polymers101,2582
Non-polymers241
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

#1: RNA chain RNA (5'-R(P*UP*UP*AP*CP*C)-3')


Mass: 1506.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Protein Piwi-like protein 1


Mass: 99751.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9JMB7, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: MIWI in complex with piRNA / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

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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: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5307495
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 374362 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7KX7

7kx7


Accession code: 7KX7 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045961
ELECTRON MICROSCOPYf_angle_d0.6098112
ELECTRON MICROSCOPYf_dihedral_angle_d5.094869
ELECTRON MICROSCOPYf_chiral_restr0.044920
ELECTRON MICROSCOPYf_plane_restr0.0041016

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