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- PDB-9iiy: Cryo-EM Structure of EfPiwi-piRNA-target (25-nt, bilobed) -

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Basic information

Entry
Database: PDB / ID: 9iiy
TitleCryo-EM Structure of EfPiwi-piRNA-target (25-nt, bilobed)
Components
  • Piwi
  • RNA (5'-R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)-3')
  • RNA (5'-R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / Piwi protein / Pi-RNA / Argonaute / 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
RNA / RNA (> 10) / Piwi
Similarity search - Component
Biological speciesEphydatia fluviatilis (invertebrata)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLi, Z.Q. / Xu, Q.K. / Wu, J.P. / Shen, E.Z.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2024
Title: Structural insights into RNA cleavage by PIWI Argonaute
Authors: Li, Z.Q. / Xu, Q.K. / Wu, J.P. / Shen, E.Z.
History
DepositionJun 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Piwi
B: RNA (5'-R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G)-3')
C: RNA (5'-R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)124,3443
Polymers124,3443
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Piwi


Mass: 110611.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ephydatia fluviatilis (invertebrata) / Gene: EfPiwiA / Production host: Homo sapiens (human) / References: UniProt: D5MRY8
#2: RNA chain RNA (5'-R(P*UP*AP*GP*CP*AP*GP*AP*UP*CP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*AP*CP*G)-3')


Mass: 7099.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*CP*GP*UP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*GP*AP*UP*CP*AP*GP*CP*U)-3')


Mass: 6632.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: EfPiwi-piRNA-target (25-nt, bilobed) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Ephydatia fluviatilis (invertebrata)31330
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87581 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026154
ELECTRON MICROSCOPYf_angle_d0.7758526
ELECTRON MICROSCOPYf_dihedral_angle_d14.5151195
ELECTRON MICROSCOPYf_chiral_restr0.075993
ELECTRON MICROSCOPYf_plane_restr0.005926

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