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- EMDB-18878: Cryo-EM structure of the Asgard archaeal Argonaute HrAgo1 bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-18878
TitleCryo-EM structure of the Asgard archaeal Argonaute HrAgo1 bound to a guide RNA
Map data
Sample
  • Complex: Asgard archaeal Argonaute HrAgo1 in complex with the 5'-end of a guide RNA
    • Protein or peptide: HrAgo1
    • RNA: RNA (5'-R(P*UP*GP*AP*GP*GP*U*(MG))-3')
  • Ligand: MAGNESIUM ION
KeywordsArgonaute / RNA / RNA BINDING PROTEIN
Biological speciesCandidatus Harpocratesius repetitus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFinocchio G / Swarts D / Jinek M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2024
Title: RNA-guided RNA silencing by an Asgard archaeal Argonaute.
Authors: Carolien Bastiaanssen / Pilar Bobadilla Ugarte / Kijun Kim / Giada Finocchio / Yanlei Feng / Todd A Anzelon / Stephan Köstlbacher / Daniel Tamarit / Thijs J G Ettema / Martin Jinek / Ian J ...Authors: Carolien Bastiaanssen / Pilar Bobadilla Ugarte / Kijun Kim / Giada Finocchio / Yanlei Feng / Todd A Anzelon / Stephan Köstlbacher / Daniel Tamarit / Thijs J G Ettema / Martin Jinek / Ian J MacRae / Chirlmin Joo / Daan C Swarts / Fabai Wu /
Abstract: Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic ...Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon 'Candidatus Harpocratesius repetitus' shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.
History
DepositionNov 10, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18878.png

Downloads & links

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Map

FileDownload / File: emd_18878.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Contour LevelBy AUTHOR: 0.0457
Minimum - Maximum-0.1736023 - 0.29261342
Average (Standard dev.)0.000042150816 (±0.0060169054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18878_additional_1.map
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Half map: #2

Fileemd_18878_half_map_1.map
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Half map: #1

Fileemd_18878_half_map_2.map
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Sample components

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Entire : Asgard archaeal Argonaute HrAgo1 in complex with the 5'-end of a ...

EntireName: Asgard archaeal Argonaute HrAgo1 in complex with the 5'-end of a guide RNA
Components
  • Complex: Asgard archaeal Argonaute HrAgo1 in complex with the 5'-end of a guide RNA
    • Protein or peptide: HrAgo1
    • RNA: RNA (5'-R(P*UP*GP*AP*GP*GP*U*(MG))-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Asgard archaeal Argonaute HrAgo1 in complex with the 5'-end of a ...

SupramoleculeName: Asgard archaeal Argonaute HrAgo1 in complex with the 5'-end of a guide RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Harpocratesius repetitus (archaea)

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Macromolecule #1: HrAgo1

MacromoleculeName: HrAgo1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Harpocratesius repetitus (archaea)
Molecular weightTheoretical: 95.369859 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSKSQNKGRK SNDAPLASPC CPQKKKIDLE MNLFPVKISN LKISIYSWLI FPKIDNYKVQ RNILEIALSE EALYEYIIQK NKIYQKKRH PNIKRVVLFQ NKEFQIEINH LETVYLLDNP TLQNEIFGSI CQTVGFEQIG HNYYYSAERQ SSQLTQSTKE S LKRIFPAI ...String:
MSKSQNKGRK SNDAPLASPC CPQKKKIDLE MNLFPVKISN LKISIYSWLI FPKIDNYKVQ RNILEIALSE EALYEYIIQK NKIYQKKRH PNIKRVVLFQ NKEFQIEINH LETVYLLDNP TLQNEIFGSI CQTVGFEQIG HNYYYSAERQ SSQLTQSTKE S LKRIFPAI EIDGGKYYLK QGLTTAIHST KKNFSIDQGK NAISNVVELE QTSKLIQKKN LLEIIMDLNR KVKDHHKIEN LL IGSRFIT HYNNRIYTIH GIAWNKDPTS TFQIRSKLHQ NLEITFEEYY KKNYQLKISD LHQPLIIYYP MSSQKSATSS GSQ DILYFL PEFCHLFGLS NLDADNFRIR QEITRNTQMS PSDRYRKLKT FVENQDILEF FKVWGLDIDS RMISMSGIKL PSLE IQTQT GVFPINFEQS NWLSLLNRSQ VIDAPELKKW MILYPKKSMS LQEARKFSND FQKIAQQMGM VCRPPQLQGV FDMTK FLAI LKKNPSQHHI NSIQLILTIT PNRNKTCYRK IKQLCYRDLG IANQNVVLKN LRDQKRRMPI IRNLVRQIIC KVPNFN TKY GGALWKIKNN SIPDKTLIVG IDVWHGRPGI DKSIAGIVFS TDKGLHYTAN YTITPRKGLE FIHNLGKIII TQLQNHY NA TRQYFENILI FRDGVGNTQY NKILQEEFKS IQQELTNSSI FSEKHPKIAI ILVNKRINRR LFHKNKQGQI LNPKPGTF I EDQYIKSEFS NYYLVPHFSR FGTTRPIHIS VIYNNTKYVN FQFVEIANIL CHLNYNWAGT VRIPASVEYA HKVADFIGS NQITSIAPEL LQTQFYL

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Macromolecule #2: RNA (5'-R(P*UP*GP*AP*GP*GP*U*(MG))-3')

MacromoleculeName: RNA (5'-R(P*UP*GP*AP*GP*GP*U*(MG))-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Candidatus Harpocratesius repetitus (archaea)
Molecular weightTheoretical: 6.812045 KDa
SequenceString:
UGAGGUAGUA GGUUGUAUAG U

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.81 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Model generated with Alphafold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283659
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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