[English] 日本語
Yorodumi
- EMDB-54428: Cryo-EM structure of the endogeneous MIWI in complex with pachyte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54428
TitleCryo-EM structure of the endogeneous MIWI in complex with pachytene piRNA at 3A
Map data
Sample
  • Complex: MIWI in complex with piRNA
    • Protein or peptide: Piwi-like protein 1
    • RNA: RNA
  • Ligand: MAGNESIUM ION
KeywordsMIWI / PIWIL1 / piRNA / slicer / pachytene piRNA / RNA BINDING PROTEIN
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
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRaad NG / Fernandez-Rodriguez C / Pandey RR / Mohammed I / Uchikawa E / Burger F / Homolka D / Pillai RS
Funding support Switzerland, 3 items
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 17, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54428.png

Downloads & links

-
Map

FileDownload / File: emd_54428.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 224 pix.
= 327.936 Å		1.46 Å/pix.
x 224 pix.
= 327.936 Å		1.46 Å/pix.
x 224 pix.
= 327.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.5843423 - 1.2715658
Average (Standard dev.)0.0004683902 (±0.019105317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 327.936 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_54428_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54428_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MIWI in complex with piRNA

EntireName: MIWI in complex with piRNA
Components
  • Complex: MIWI in complex with piRNA
    • Protein or peptide: Piwi-like protein 1
    • RNA: RNA
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: MIWI in complex with piRNA

SupramoleculeName: MIWI in complex with piRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Piwi-like protein 1

MacromoleculeName: Piwi-like protein 1 / 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: Mus musculus (house mouse)
Molecular weightTheoretical: 99.751188 KDa
SequenceString: MTGRARARAR GRARGQETVQ HVGAAASQQP GYIPPRPQQS PTEGDLVGRG RQWSHPQFEK RGMVVGATSK SQELQISAGF QELSLAERG GRRRDFHDLG VNTRQNLDHV KESKTGSSGI IVKLSTNHFR LTSRPQWALY QYHIDYNPLM EARRLRSALL F QHEDLIGR ...String:
MTGRARARAR GRARGQETVQ HVGAAASQQP GYIPPRPQQS PTEGDLVGRG RQWSHPQFEK RGMVVGATSK SQELQISAGF QELSLAERG GRRRDFHDLG VNTRQNLDHV KESKTGSSGI IVKLSTNHFR LTSRPQWALY QYHIDYNPLM EARRLRSALL F QHEDLIGR CHAFDGTILF LPKRLQHKVT EVFSQTRNGE HVRITITLTN ELPPTSPTCL QFYNIIFRRL LKIMNLQQIG RN YYNPSDP IDIPNHRLVI WPGFTTSILQ YENNIMLCTD VSHKVLRSET VLDFMFNLYQ QTEEHKFQEQ VSKELIGLIV LTK YNNKTY RVDDIDWDQN PKSTFKKADG SEVSFLEYYR KQYNQEITDL KQPVLVSQPK RRRGPGGTLP GPAMLIPELC YLTG LTDKM RNDFNVMKDL AVHTRLTPEQ RQREVGRLID YIHKDDNVQR ELRDWGLSFD SNLLSFSGRI LQSEKIHQGG KTFDY NPQF ADWSKETRGA PLISVKPLDN WLLIYTRRNY EAANSLIQNL FKVTPAMGIQ MKKAIMIEVD DRTEAYLRAL QQKVTS DTQ IVVCLLSSNR KDKYDAIKKY LCTDCPTPSQ CVVARTLGKQ QTVMAIATKI ALQMNCKMGG ELWRVDMPLK LAMIVGI DC YHDTTAGRRS IAGFVASINE GMTRWFSRCV FQDRGQELVD GLKVCLQAAL RAWSGCNEYM PSRVIVYRDG VGDGQLKT L VNYEVPQFLD CLKSVGRGYN PRLTVIVVKK RVNARFFAQS GGRLQNPLPG TVIDVEVTRP EWYDFFIVSQ AVRSGSVSP THYNVIYDSS GLKPDHIQRL TYKLCHVYYN WPGVIRVPAP CQYAHKLAFL VGQSIHREPN LSLSNRLYYL

UniProtKB: Piwi-like protein 1

-
Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.506944 KDa
SequenceString:
UUACC

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kx7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27959
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9s0z:
Cryo-EM structure of the endogeneous MIWI in complex with pachytene piRNA at 3A

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more