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- PDB-9ij3: Cryo-EM Structure of MILI-piRNA-target (26-nt) -

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Basic information

Entry
Database: PDB / ID: 9ij3
TitleCryo-EM Structure of MILI-piRNA-target (26-nt)
Components
  • Piwi-like protein 2
  • RNA (25-MER)
  • RNA (26-MER)
KeywordsRNA BINDING PROTEIN/RNA / Piwi protein / Pi-RNA / Argonaute / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


perinucleolar chromocenter / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated DNA methylation / PET complex / pi-body / secondary piRNA processing / transposable element silencing by mRNA destabilization / positive regulation of meiosis I / piRNA binding / transposable element silencing by heterochromatin formation ...perinucleolar chromocenter / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated DNA methylation / PET complex / pi-body / secondary piRNA processing / transposable element silencing by mRNA destabilization / positive regulation of meiosis I / piRNA binding / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / positive regulation of cytoplasmic translation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / regulatory ncRNA-mediated gene silencing / P granule / oogenesis / RNA endonuclease activity / meiotic cell cycle / rhythmic process / spermatogenesis / mRNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain ...DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / 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-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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-like protein 2
B: RNA (26-MER)
C: RNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9714
Polymers125,9163
Non-polymers551
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-like protein 2


Mass: 109636.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piwil2, Mili / Production host: Homo sapiens (human)
References: UniProt: Q8CDG1, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (26-MER)


Mass: 8262.972 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 (25-MER)


Mass: 8016.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / 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: MILI-piRNA-target (26-nt) / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Mus musculus (house mouse)10090
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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139074 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047262
ELECTRON MICROSCOPYf_angle_d0.92810079
ELECTRON MICROSCOPYf_dihedral_angle_d10.2471396
ELECTRON MICROSCOPYf_chiral_restr0.0521186
ELECTRON MICROSCOPYf_plane_restr0.0071085

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