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- EMDB-60273: Cryo-EM structure of a short prokaryotic Argonaute system from ar... -

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Basic information

Entry
Database: EMDB / ID: EMD-60273
TitleCryo-EM structure of a short prokaryotic Argonaute system from archaeon Suldolobus islandicus
Map data
Sample
  • Complex: SiAgo-SiAga1 complex
    • Protein or peptide: Piwi domain-containing protein
    • Protein or peptide: SiAgo-associated protein1, SiAga1
    • RNA: RNA (5'-R(P*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*GP*A)-3')
    • DNA: DNA (5'-D(*CP*CP*TP*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*A)-3')
  • Ligand: MAGNESIUM ION
KeywordsArgonaute / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Function / homologyPiwi domain / Piwi domain / Piwi / Ribonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / Uncharacterized protein / Piwi domain-containing protein
Function and homology information
Biological speciesSulfolobus islandicus (strain M.16.4 / Kamchatka #3) (archaea) / Saccharolobus islandicus M.16.4 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDai ZK / Guan ZY / Han WY / Zou TT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus.
Authors: Zhikang Dai / Yu Chen / Zeyuan Guan / Xueting Chen / Keyi Tan / Kaiyue Yang / Xuhui Yan / Yidong Liu / Zhou Gong / Wenyuan Han / Tingting Zou /
Abstract: Prokaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting ...Prokaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting invading nucleic acids. However, the activation mechanism of the SiAgo system, comprising a short pAgo from the archaeon Sulfolobus islandicus and its associated proteins SiAga1 and SiAga2, remains largely unknown. Here, we determined the cryo-electron microscopy structures of the SiAgo-Aga1 apo complex and the RNA-DNA-bound SiAgo-Aga1 complex at resolutions of 2.7 and 3.0 Å, respectively. Our results revealed that a positively charged pocket is generated from the interaction between SiAgo and SiAga1, exhibiting an architecture similar to APAZ-pAgo of short pAgo systems and accommodating the nucleic acids. Further investigation elucidated the conserved mechanism of nucleic acid recognition by SiAgo-Aga1. Both the SiAgo-Aga1 interaction and nucleic acid recognition by the complex are essential for antiviral defense. Biochemical and structural analyses demonstrated that SiAgo-Aga1 undergoes extensive conformational changes upon binding to the RNA-DNA duplex, thereby licensing its interaction with the effector SiAga2 to trigger the immune response. Overall, our findings highlight the evolutionary conservation of Agos across phylogenetic clades and provide structural insights into the activation mechanism of the SiAgo system.
History
DepositionMay 27, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60273.png

Downloads & links

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Map

FileDownload / File: emd_60273.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.8642917 - 4.289217
Average (Standard dev.)-0.00094266667 (±0.08467085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60273_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60273_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : SiAgo-SiAga1 complex

EntireName: SiAgo-SiAga1 complex
Components
  • Complex: SiAgo-SiAga1 complex
    • Protein or peptide: Piwi domain-containing protein
    • Protein or peptide: SiAgo-associated protein1, SiAga1
    • RNA: RNA (5'-R(P*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*GP*A)-3')
    • DNA: DNA (5'-D(*CP*CP*TP*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*A)-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SiAgo-SiAga1 complex

SupramoleculeName: SiAgo-SiAga1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Sulfolobus islandicus (strain M.16.4 / Kamchatka #3) (archaea)

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Macromolecule #1: Piwi domain-containing protein

MacromoleculeName: Piwi domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus islandicus M.16.4 (archaea)
Molecular weightTheoretical: 52.741414 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSEYATILPE NKINVIFRSN NKYHVPEFIT VFKPYEGRDI NLQVLVVNGD NEIYDLTKLL FYEIYVKDDT KYPWPYTKTR GGISRVFGI RYNFDPSTIS RININSENDF ISSISNQLDM NRFNVAVIIA NRKLTKEFHD KTKAALIGSR IRTQFVTFTT L KRLKNRKY ...String:
MSEYATILPE NKINVIFRSN NKYHVPEFIT VFKPYEGRDI NLQVLVVNGD NEIYDLTKLL FYEIYVKDDT KYPWPYTKTR GGISRVFGI RYNFDPSTIS RININSENDF ISSISNQLDM NRFNVAVIIA NRKLTKEFHD KTKAALIGSR IRTQFVTFTT L KRLKNRKY KATIPLPLAV QLIAKAGGTP WIVDSSIYND LSKNVSSNGM LMGIAFARTR KDKITYSVGY FTTLNNYYQR FD VQPINES APITDSTEGL YVPKEAMVKT LESGIGWYKN IIGITPPLLI IFKTSPMHKD EKEAIEAVLG KDIKWVFIHA QYN TPVRIF GNKEDDYKVN RGTVIIKKRK RWNPNNGDYL HSEIVITATG KYRKPSTKNP SETEERYISG TPRPITLNVY SSFD VNPIG VAELTLSQIK ADWEHPDIRK RKITVLKYAN RMAKIIQYIN NLSSVPSVDV RDVL

UniProtKB: Piwi domain-containing protein

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Macromolecule #2: SiAgo-associated protein1, SiAga1

MacromoleculeName: SiAgo-associated protein1, SiAga1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus islandicus M.16.4 (archaea)
Molecular weightTheoretical: 29.133615 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVLESNMFKT EQELPELIVN CIEIDNEKEA HKVVKEISKY GIFGVVREKK IFFTTVIEDD DFLKDRLTEV LKNYNINFSD IKKNCKKII PEDNKDYFSQ IFLNALRYVI YQKLEDINKD KKENERWTIN ESEDGVYICK ERYDIDNYKI CVGAKFTIKV F DNKAELYV ...String:
MVLESNMFKT EQELPELIVN CIEIDNEKEA HKVVKEISKY GIFGVVREKK IFFTTVIEDD DFLKDRLTEV LKNYNINFSD IKKNCKKII PEDNKDYFSQ IFLNALRYVI YQKLEDINKD KKENERWTIN ESEDGVYICK ERYDIDNYKI CVGAKFTIKV F DNKAELYV DRKLKLYDED KKLTRKLRGK INKMSVVEPK TRYEFIREII QEISGNFDYI NIKLSKDYTV NMTRTKLNEK LP TPF

UniProtKB: Uncharacterized protein

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

MacromoleculeName: RNA (5'-R(P*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*GP*A)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Saccharolobus islandicus M.16.4 (archaea)
Molecular weightTheoretical: 6.697044 KDa
SequenceString:
UCAAAGCUUA GAUACCCUGG A

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Macromolecule #4: DNA (5'-D(*CP*CP*TP*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*...

MacromoleculeName: DNA (5'-D(*CP*CP*TP*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*A)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharolobus islandicus M.16.4 (archaea)
Molecular weightTheoretical: 7.344753 KDa
SequenceString:
(DC)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DG)(DT) (DA)(DT)(DC)(DT)(DA)(DA)(DG)(DC)(DT)(DT) (DT)(DG)(DA)(DA)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 388934
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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