+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36385 | ||||||||||||
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Title | Cryo-EM structure of the prokaryotic SPARSA system complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | the SPARSA antiviral system / NADase / argonaute protein / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-DNA-RNA complex | ||||||||||||
Function / homology | SIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / Ribonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / Piwi domain protein / Sir2 superfamily protein Function and homology information | ||||||||||||
Biological species | Geobacter sulfurreducens PCA (bacteria) / Geobacter sulfurreducens (bacteria) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Xu X / Zhen X / Long F | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system. Authors: Xiangkai Zhen / Xiaolong Xu / Le Ye / Song Xie / Zhijie Huang / Sheng Yang / Yanhui Wang / Jinyu Li / Feng Long / Songying Ouyang / Abstract: Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos (eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In contrast, the functions of ...Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos (eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In contrast, the functions of prokaryotic counterparts (pAgo) are less well known. Recently, short pAgos in conjunction with the associated TIR or Sir2 (SPARTA or SPARSA) were found to serve as antiviral systems to combat phage infections. Herein, we present the cryo-EM structures of nicotinamide adenine dinucleotide (NAD)-bound SPARSA with and without nucleic acids at resolutions of 3.1 Å and 3.6 Å, respectively. Our results reveal that the APAZ (Analogue of PAZ) domain and the short pAgo form a featured architecture similar to the long pAgo to accommodate nucleic acids. We further identified the key residues for NAD binding and elucidated the structural basis for guide RNA and target DNA recognition. Using structural comparisons, molecular dynamics simulations, and biochemical experiments, we proposed a putative mechanism for NAD hydrolysis in which an H186 loop mediates nucleophilic attack by catalytic water molecules. Overall, our study provides mechanistic insight into the antiphage role of the SPARSA system. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36385.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-36385-v30.xml emd-36385.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36385_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_36385.png | 118.9 KB | ||
Masks | emd_36385_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-36385.cif.gz | 6.9 KB | ||
Others | emd_36385_half_map_1.map.gz emd_36385_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36385 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36385 | HTTPS FTP |
-Validation report
Summary document | emd_36385_validation.pdf.gz | 853.7 KB | Display | EMDB validaton report |
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Full document | emd_36385_full_validation.pdf.gz | 853.3 KB | Display | |
Data in XML | emd_36385_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_36385_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36385 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36385 | HTTPS FTP |
-Related structure data
Related structure data | 8jl0MC 8jkzC 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_36385.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36385_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36385_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36385_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the Sir2/Ago/Guide RNA/recognition DNA complex
Entire | Name: the Sir2/Ago/Guide RNA/recognition DNA complex |
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Components |
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-Supramolecule #1: the Sir2/Ago/Guide RNA/recognition DNA complex
Supramolecule | Name: the Sir2/Ago/Guide RNA/recognition DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Geobacter sulfurreducens PCA (bacteria) |
-Supramolecule #2: Sir2
Supramolecule | Name: Sir2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Geobacter sulfurreducens PCA (bacteria) |
-Supramolecule #3: Ago
Supramolecule | Name: Ago / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Supramolecule #4: DNA/guide RNA duplex
Supramolecule | Name: DNA/guide RNA duplex / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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-Macromolecule #1: Sir2 superfamily protein
Macromolecule | Name: Sir2 superfamily protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Molecular weight | Theoretical: 66.488727 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDVLTDNEFY QHYLQNSQHM MWFLGAGTSR SAGLPTASDI IWDLKHRYYC LHENQDYQKH DINNHAIKSK IQSYMDSKGF PLQWSPEEY SFYFELVFRD DYEAQRKYLL EALASRKVSL NIGHRVLAAL LEMNQTKVVF TTNFDDVIET AFSDISGKHL S VYHLEGSY ...String: MDVLTDNEFY QHYLQNSQHM MWFLGAGTSR SAGLPTASDI IWDLKHRYYC LHENQDYQKH DINNHAIKSK IQSYMDSKGF PLQWSPEEY SFYFELVFRD DYEAQRKYLL EALASRKVSL NIGHRVLAAL LEMNQTKVVF TTNFDDVIET AFSDISGKHL S VYHLEGSY AALSALNTEA FPIYAKIHGD FRYQKIKNLT PDLQTNDREI HKCFLAAAIR FGLVVSGYSG RDENVMTMLR AA IDQNNAF PHGLYWTVPS ISKSEPAVQD LITYAQGKGV RAYLVETGTF DEMLSKIWRQ VKDKPAAIDA KVRTARVCPV SIP LPGPGK SFPALRTNAL PVVTQSIRCG VVTLASPITF SELKERISQK SPKALLTYTE KVLFLGGEPE IRKIFSNDEI NSIG QYYID EIAQSVAAST FLKSFVEEAI LTALLREKPI LHRVRHRTHY AVIPNASAKD DRFLDLRKAV GFKGDLGYIT GNVTN AKEL SWAEAVSIRL EERGGKLWIM LKPEIWIKPL DRREEATDFI RSRRRYRFNQ CSYQILDAWI KILFGSIGGG GTVNIS CFP DAEFKAEFEI GTRTAFSLGV GYG UniProtKB: Sir2 superfamily protein |
-Macromolecule #2: Piwi domain protein
Macromolecule | Name: Piwi domain protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Molecular weight | Theoretical: 53.325566 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MADNLSQLAA HSTIPEPLLL FKDNRTDTHP LRGLSQYGPY SACFNLPGQV RLAYLAPTEH MRKLDAIVRE LQNPATPKEA TNYYVEYGG FEKVFKVPLV MPQEHLRCLA LDECHGVAAN GNGLALADKI VQSMSGLFRQ KHAFDVLLVY LPASWKKCFE Y DGFDLHDR ...String: MADNLSQLAA HSTIPEPLLL FKDNRTDTHP LRGLSQYGPY SACFNLPGQV RLAYLAPTEH MRKLDAIVRE LQNPATPKEA TNYYVEYGG FEKVFKVPLV MPQEHLRCLA LDECHGVAAN GNGLALADKI VQSMSGLFRQ KHAFDVLLVY LPASWKKCFE Y DGFDLHDR IKAKVAPLNL PIQIINDTAL TRQCRANVMW GVSVALYAKA GGIPWKLADW DKDEAYIGLS YAIKKNAEGQ EY TTCCSQV FDPDGTGFEF VAYDTREFIT DRKGNPYLSY QEMQSVLSKS LHLYQSSHNG RMPRKIFIHK TTHFTEDEIQ GAF DSFSSS TEIELVQIIQ STNWYGLKVD GKKGDKPVAP ASYPVDRGLY QPLTESECLL WTQGSVMGVN QQNPGQPVFK EAAL TPLPN PIMLRRFSGN GGWHATCSSI LALTKVDWNN NTLYKKLPVT LVYSQVFADV VKQTPEIVNE IYDYRFFM UniProtKB: Piwi domain protein |
-Macromolecule #3: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*TP*CP*TP*AP*AP*GP*AP*AP*AP*CP*CP*AP...
Macromolecule | Name: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*TP*CP*TP*AP*AP*GP*AP*AP*AP*CP*CP*AP*TP*TP*AP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 6.728394 KDa |
Sequence | String: (DA)(DC)(DG)(DA)(DC)(DG)(DT)(DC)(DT)(DA) (DA)(DG)(DA)(DA)(DA)(DC)(DC)(DA)(DT)(DT) (DA)(DT) |
-Macromolecule #4: RNA (5'-R(P*AP*UP*AP*AP*UP*GP*GP*UP*UP*UP*CP*UP*UP*AP*GP*AP*CP*GP...
Macromolecule | Name: RNA (5'-R(P*AP*UP*AP*AP*UP*GP*GP*UP*UP*UP*CP*UP*UP*AP*GP*AP*CP*GP*UP*CP*GP*U)-3') type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 6.998139 KDa |
Sequence | String: AUAAUGGUUU CUUAGACGUC GU |
-Macromolecule #5: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Software | Name: EPU (ver. FEI) |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8jl0: |