+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37457 | |||||||||
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Title | Cryo-EM structure of TtdAgo-guide DNA-target DNA complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA BINDING PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Zhuang L | |||||||||
Funding support | 1 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute. Authors: Longyu Wang / Wanping Chen / Chendi Zhang / Xiaochen Xie / Fuyong Huang / Miaomiao Chen / Wuxiang Mao / Na Yu / Qiang Wei / Lixin Ma / Zhuang Li / Abstract: The Argonaute nuclease from the thermophilic archaeon Pyrococcus furiosus (PfAgo) contributes to host defense and represents a promising biotechnology tool. Here, we report the structure of a PfAgo- ...The Argonaute nuclease from the thermophilic archaeon Pyrococcus furiosus (PfAgo) contributes to host defense and represents a promising biotechnology tool. Here, we report the structure of a PfAgo-guide DNA-target DNA ternary complex at the cleavage-compatible state. The ternary complex is predominantly dimerized, and the dimerization is solely mediated by PfAgo at PIWI-MID, PIWI-PIWI, and PAZ-N interfaces. Additionally, PfAgo accommodates a short 14-bp guide-target DNA duplex with a wedge-type N domain and specifically recognizes 5'-phosphorylated guide DNA. In contrast, the PfAgo-guide DNA binary complex is monomeric, and the engagement of target DNA with 14-bp complementarity induces sufficient dimerization and activation of PfAgo, accompanied by movement of PAZ and N domains. A closely related Argonaute from Thermococcus thioreducens adopts a similar dimerization configuration with an additional zinc finger formed at the dimerization interface. Dimerization of both Argonautes stabilizes the catalytic loops, highlighting the important role of Argonaute dimerization in the activation and target cleavage. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37457.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-37457-v30.xml emd-37457.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37457_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_37457.png | 88.3 KB | ||
Filedesc metadata | emd-37457.cif.gz | 6 KB | ||
Others | emd_37457_half_map_1.map.gz emd_37457_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37457 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37457 | HTTPS FTP |
-Related structure data
Related structure data | 8wd8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37457.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37457_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37457_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of TtdAgo-guide DNA-target DNA complex
Entire | Name: Cryo-EM structure of TtdAgo-guide DNA-target DNA complex |
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Components |
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-Supramolecule #1: Cryo-EM structure of TtdAgo-guide DNA-target DNA complex
Supramolecule | Name: Cryo-EM structure of TtdAgo-guide DNA-target DNA complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Supramolecule #2: DNA binding protein
Supramolecule | Name: DNA binding protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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-Macromolecule #1: Argonaute family protein
Macromolecule | Name: Argonaute family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Theoretical: 87.488398 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MLMKVLTNMV KLNQDIIPNE IYLYKIFNKP EDGMNIYKIA YRNHGIVIDP QNRIIATPSE LEYSGKFAIE DEISFNELPE NYQNRLVLR ILRDNGISDH ALSRTLQKYR KPKPFGDFEV IPEIRSSVIK HGGDFYLVLH LSHQIRSKKT LWELVGRNKD A LRDFLKEH ...String: MLMKVLTNMV KLNQDIIPNE IYLYKIFNKP EDGMNIYKIA YRNHGIVIDP QNRIIATPSE LEYSGKFAIE DEISFNELPE NYQNRLVLR ILRDNGISDH ALSRTLQKYR KPKPFGDFEV IPEIRSSVIK HGGDFYLVLH LSHQIRSKKT LWELVGRNKD A LRDFLKEH RGTILLRDIA SEHKVVYKPI FKRYNGDPDL IEDNSNDVEH WYDYHLERYW NTPELKKEFY KKFGPVDLNQ PI ILAKPLR QHNRGDLVHL LPQFVVPVYN AEQLNDILAS EILEYLKLTS NQRISLLSRL INDIKTNTNI IVSSLTELEA NTF DVDLND MLQVRNADNV KVTLSELEIS KTRLFTWMKS RKYPVILPYD IPQKLKKIEK IPVFIIVDSA LSRDIQTFAK DEFR YLISS LQKSLSNWVD FPILDIRDKY IFTIDLTSDK DIVNLSIKLV NLMKNAELGL ALIATRTKLP NETFDEVKKR LFSVN IISQ VVNEATLYKR DKYNESRLNL YVQHNLLFQI LSKLGIKYYV LRHKFSYDYI VGIDVTPMKL SHGYIGGSAV MFDSQG YIR KIIPVEIGEQ MGESIDMKEF FKDMVVQFGK FGIDLEGKSI LILRDGKITK DEEEGLAYIS KVFGIKITTF NIVKRHL LR IFANRKLYLR LANSVYLLPH RIKQSVGTPV PLKLSEKRLI LDGTITSQEI TYNDIFEILL LSELNYGSIS ADMKLPAP V HYAHKFVRAL RKGWRIREEL LAEGFLYFV UniProtKB: Argonaute family protein |
-Macromolecule #2: Target DNA
Macromolecule | Name: Target DNA / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Theoretical: 5.051302 KDa |
Sequence | String: (DA)(DC)(DA)(DA)(DC)(DC)(DT)(DA)(DC)(DT) (DA)(DC)(DC)(DT)(DC)(DC)(DT) |
-Macromolecule #3: Guide DNA
Macromolecule | Name: Guide DNA / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Theoretical: 5.049273 KDa |
Sequence | String: (DG)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA) (DG)(DG)(DT)(DT)(DG)(DT) |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |