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- EMDB-60612: Cryo-EM Structure of MILI-piRNA-target (22-nt, bilobed) -

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Basic information

Entry
Database: EMDB / ID: EMD-60612
TitleCryo-EM Structure of MILI-piRNA-target (22-nt, bilobed)
Map data
Sample
  • Complex: MILI-piRNA-target (22-nt, bilobed)
    • Protein or peptide: Piwi-like protein 2
    • RNA: RNA (26-MER)
    • RNA: RNA (5'-R(P*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')
  • Ligand: MAGNESIUM ION
KeywordsPiwi protein / Pi-RNA / Argonaute / RNA BINDING PROTEIN/RNA / 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
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi ZQ / Xu QK / Wu JP / Shen EZ
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2024
Title: Structural insights into RNA cleavage by PIWI Argonaute
Authors: Li ZQ / Xu QK / Wu JP / Shen EZ
History
DepositionJun 21, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60612.png

Downloads & links

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Map

FileDownload / File: emd_60612.map.gz / Format: CCP4 / Size: 13.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 152 pix.
= 173.28 Å		1.14 Å/pix.
x 152 pix.
= 173.28 Å		1.14 Å/pix.
x 152 pix.
= 173.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.6696102 - 1.1658187
Average (Standard dev.)0.0007727642 (±0.03379328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions152152152
Spacing152152152
CellA=B=C: 173.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60612_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60612_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MILI-piRNA-target (22-nt, bilobed)

EntireName: MILI-piRNA-target (22-nt, bilobed)
Components
  • Complex: MILI-piRNA-target (22-nt, bilobed)
    • Protein or peptide: Piwi-like protein 2
    • RNA: RNA (26-MER)
    • RNA: RNA (5'-R(P*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: MILI-piRNA-target (22-nt, bilobed)

SupramoleculeName: MILI-piRNA-target (22-nt, bilobed) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Piwi-like protein 2

MacromoleculeName: Piwi-like protein 2 / 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: 109.636406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDPVRPLFRG PTPVHPSQCV RMPGCWPQAP RPLEPAWGRA GPAGRGLVFR KPEDSSPPLQ PVQKDSVGLV SMFRGMGLDT AFRPPSKRE VPPLGRGVLG RGLSANMVRK DREEPRSSLP DPSVLAAGDS KLAEASVGWS RMLGRGSSEV SLLPLGRAAS S IGRGMDKP ...String:
MDPVRPLFRG PTPVHPSQCV RMPGCWPQAP RPLEPAWGRA GPAGRGLVFR KPEDSSPPLQ PVQKDSVGLV SMFRGMGLDT AFRPPSKRE VPPLGRGVLG RGLSANMVRK DREEPRSSLP DPSVLAAGDS KLAEASVGWS RMLGRGSSEV SLLPLGRAAS S IGRGMDKP PSAFGLTARD PPRLPQPPAL SPTSLHSADP PPVLTMERKE KELLVKQGSK GTPQSLGLNL IKIQCHNEAV YQ YHVTFSP SVECKSMRFG MLKDHQSVTG NVTAFDGSIL YLPVKLQQVV ELKSQRKTDD AEISIKIQLT KILEPCSDLC IPF YNVVFR RVMKLLDMKL VGRNFYDPTS AMVLQQHRLQ IWPGYAASIR RTDGGLFLLA DVSHKVIRND SVLDVMHAIY QQNK EHFQD ECSKLLVGSI VITRYNNRTY RIDDVDWNKT PKDSFVMSDG KEITFLEYYS KNYGITVKED DQPLLIHRPS ERQNN HGML LKGEILLLPE LSFMTGIPEK MKKDFRAMKD LTQQINLSPK QHHGALECLL QRISQNETAS NELTRWGLSL HKDVHK IEG RLLPMERINL RNTSFVTSED LNWVKEVTRD ASILTIPMHF WALFYPKRAM DQARELVNML EKIAGPIGMR ISPPAWV EL KDDRIETYIR TIQSLLGVEG KIQMVVCIIM GTRDDLYGAI KKLCCVQSPV PSQVINVRTI GQPTRLRSVA QKILLQMN C KLGGELWGVD IPLKQLMVIG MDVYHDPSRG MRSVVGFVAS INLTLTKWYS RVVFQMPHQE IVDSLKLCLV GSLKKYYEV NHCLPEKIVV YRDGVSDGQL KTVANYEIPQ LQKCFEAFDN YHPKMVVFVV QKKISTNLYL AAPDHFVTPS PGTVVDHTIT SCEWVDFYL LAHHVRQGCG IPTHYICVLN TANLSPDHMQ RLTFKLCHMY WNWPGTIRVP APCKYAHKLA FLSGQILHHE P AIQLCGNL FFL

UniProtKB: Piwi-like protein 2

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Macromolecule #2: RNA (26-MER)

MacromoleculeName: RNA (26-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.262972 KDa
SequenceString:
UUACCAUCAA CAUGGAAACU UGGCU(OMC)

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Macromolecule #3: RNA (5'-R(P*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP...

MacromoleculeName: RNA (5'-R(P*CP*AP*AP*GP*UP*UP*UP*CP*CP*AP*UP*GP*UP*UP*GP*AP*UP*GP*GP*UP*A)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.691974 KDa
SequenceString:
CAAGUUUCCA UGUUGAUGGU A

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122269
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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