[English] 日本語
Yorodumi
- EMDB-33809: Cryo-EM structure of the EfPiwi(N959K) in complex with piRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33809
TitleCryo-EM structure of the EfPiwi(N959K) in complex with piRNA
Map dataoverall map
Sample
  • Complex: EfPiwi(N959K)-piRNA
    • Complex: EfPiwi(N959K)
      • Protein or peptide: Piwi
    • Complex: piRNA
      • RNA: piRNA
  • Ligand: MAGNESIUM ION
KeywordspiRNA / Piwi protein / Argonaute / RNA binding protein / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


piRNA binding / regulatory ncRNA-mediated gene silencing / P granule / RNA endonuclease activity
Similarity search - Function
Piwi domain / Piwi domain profile. / 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 speciesEphydatia fluviatilis (invertebrata) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi ZQ / Liu HB / Wu JP / Shen EZ
Funding support China, 1 items
OrganizationGrant numberCountry
Other privateWestlake Education Foundation (101486021901) China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target silencing.
Authors: Zhiqing Li / Zhenzhen Li / Yuqi Zhang / Lunni Zhou / Qikui Xu / Lili Li / Lin Zeng / Junchao Xue / Huilin Niu / Jing Zhong / Qilu Yu / Dengfeng Li / Miao Gui / Yongping Huang / Shikui Tu / ...Authors: Zhiqing Li / Zhenzhen Li / Yuqi Zhang / Lunni Zhou / Qikui Xu / Lili Li / Lin Zeng / Junchao Xue / Huilin Niu / Jing Zhong / Qilu Yu / Dengfeng Li / Miao Gui / Yongping Huang / Shikui Tu / Zhao Zhang / Chun-Qing Song / Jianping Wu / En-Zhi Shen /
Abstract: The PIWI-interacting RNA (piRNA) pathway is an adaptive defense system wherein piRNAs guide PIWI family Argonaute proteins to recognize and silence ever-evolving selfish genetic elements and ensure ...The PIWI-interacting RNA (piRNA) pathway is an adaptive defense system wherein piRNAs guide PIWI family Argonaute proteins to recognize and silence ever-evolving selfish genetic elements and ensure genome integrity. Driven by this intensive host-pathogen arms race, the piRNA pathway and its targeted transposons have coevolved rapidly in a species-specific manner, but how the piRNA pathway adapts specifically to target silencing in mammals remains elusive. Here, we show that mouse MILI and human HILI piRNA-induced silencing complexes (piRISCs) bind and cleave targets more efficiently than their invertebrate counterparts from the sponge Ephydatia fluviatilis. The inherent functional differences comport with structural features identified by cryo-EM studies of piRISCs. In the absence of target, MILI and HILI piRISCs adopt a wider nucleic-acid-binding channel and display an extended prearranged piRNA seed as compared with EfPiwi piRISC, consistent with their ability to capture targets more efficiently than EfPiwi piRISC. In the presence of target, the seed gate-which enforces seed-target fidelity in microRNA RISC-adopts a relaxed state in mammalian piRISC, revealing how MILI and HILI tolerate seed-target mismatches to broaden the target spectrum. A vertebrate-specific lysine distorts the piRNA seed, shifting the trajectory of the piRNA-target duplex out of the central cleft and toward the PAZ lobe. Functional analyses reveal that this lysine promotes target binding and cleavage. Our study therefore provides a molecular basis for the piRNA targeting mechanism in mice and humans, and suggests that mammalian piRNA machinery can achieve broad target silencing using a limited supply of piRNA species.
History
DepositionJul 11, 2022-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33809.png

Downloads & links

-
Map

FileDownload / File: emd_33809.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-7.529385 - 8.983847000000001
Average (Standard dev.)-0.0016329141 (±0.17490436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: DeepEMhancer processed map

Fileemd_33809_additional_1.map
AnnotationDeepEMhancer processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_33809_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_33809_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EfPiwi(N959K)-piRNA

EntireName: EfPiwi(N959K)-piRNA
Components
  • Complex: EfPiwi(N959K)-piRNA
    • Complex: EfPiwi(N959K)
      • Protein or peptide: Piwi
    • Complex: piRNA
      • RNA: piRNA
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: EfPiwi(N959K)-piRNA

SupramoleculeName: EfPiwi(N959K)-piRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: EfPiwi(N959K)

SupramoleculeName: EfPiwi(N959K) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Ephydatia fluviatilis (invertebrata)

-
Supramolecule #3: piRNA

SupramoleculeName: piRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

-
Macromolecule #1: piRNA

MacromoleculeName: piRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.957792 KDa
SequenceString:
UUACCAUCAA CAUGGAAACU UGGC(OMU)

-
Macromolecule #2: Piwi

MacromoleculeName: Piwi / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ephydatia fluviatilis (invertebrata)
Molecular weightTheoretical: 92.654094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGSL NVESSMVSQR GSSGQPVPVS ANYLPLKGNM DGVFKYAVGF NPPVEDIRS RSQLLNEHKE LIGLTRVFDG STLYVPKRIC EQRLDLMSTR QTDGASIKVT ISLVDSVKNR DVVQLMNVIF K RILRSLKL ...String:
MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SENLYFQGSL NVESSMVSQR GSSGQPVPVS ANYLPLKGNM DGVFKYAVGF NPPVEDIRS RSQLLNEHKE LIGLTRVFDG STLYVPKRIC EQRLDLMSTR QTDGASIKVT ISLVDSVKNR DVVQLMNVIF K RILRSLKL QRIGRDYYDA NSPLEVPQHK MQLWPGYVTA INRHEGGLML VLDVSHRVMK TDTALDFLYE LYHFNQDKFR EE AFKQLVG SVVLTRYNNR TYEIDDIAWD KNPRCAFQDH AGSQITFVDY YKRAYDLDIT DLEQPLLIHR PKKKQRGKQD EGR KEVEEM VCLVPELCAM TGLTDAARSD FKVMKDLAVH TRVPPEKRAE SFRKFIQRLN TTKEASELLH SWGLVLDSRM LDMQ GRRLP PEKILFKHSS IVANMEADWS RECLKEHVIS AVSLLDWAVL FVRKDQGKAT DFVNMLSKVC PPIGMEVHEP KMVEV VNDR TESYLRALRE LIAPRLQMVV IVFPTSRDDR YSAVKKLCCI ESPIPSQVLI ARTITQQQKL RSVAQKVALQ MNAKLG GEL WAVEIPLKSC MVVGIDVYHD KSYGNKSIAG FVASTNPSFT RWYSRTAMQE QSQELIHELK LCMQAALKKY NEMNQSL PE RIIVFRDGVG EGREEYVSEF EVPQFNSCFS IFGENYCPKL AVVVVQKRIT TRIFGRSGHS YDNPPPGVIV DHTITKSY D FYLVSQHVRQ GTVSPTYYRV IYDKSGLKPD HLQRLTYKLT HMYYNWPGTI RTPAPCKYAH KLAFLVGKSL HRDPAHELS DRLFFL

UniProtKB: Piwi

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359119
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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