+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45526 | |||||||||
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Title | Parasitella parasitica Fanzor (PpFz) State 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Fanzor / Eukaryotic / RNA-guided / nuclease / Gene editing / RNA BINDING PROTEIN-ISOMERASE-RNA-DNA complex | |||||||||
Function / homology | Function and homology information Set3 complex / negative regulation of meiotic nuclear division / ascospore formation / positive regulation of meiotic nuclear division / cyclosporin A binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport ...Set3 complex / negative regulation of meiotic nuclear division / ascospore formation / positive regulation of meiotic nuclear division / cyclosporin A binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / protein peptidyl-prolyl isomerization / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to starvation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mitochondrial intermembrane space / protein transport / protein folding / outer membrane-bounded periplasmic space / periplasmic space / mRNA binding / DNA damage response / mitochondrion / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Parasitella parasitica (fungus) / Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
Authors | Xu P / Saito M / Zhang F | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2024 Title: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Authors: Peiyu Xu / Makoto Saito / Guilhem Faure / Samantha Maguire / Samuel Chau-Duy-Tam Vo / Max E Wilkinson / Huihui Kuang / Bing Wang / William J Rice / Rhiannon K Macrae / Feng Zhang / Abstract: Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different ...Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different organisms. We find that Fzs share a common ωRNA interaction interface, regardless of the length of the ωRNA, which varies considerably across species. The analysis also reveals Fz's mode of DNA recognition and unwinding capabilities as well as the presence of a non-canonical catalytic site. The structures demonstrate how protein conformations of Fz shift to allow the binding of double-stranded DNA to the active site within the R-loop. Mechanistically, examination of structures in different states shows that the conformation of the lid loop on the RuvC domain is controlled by the formation of the guide/DNA heteroduplex, regulating the activation of nuclease and DNA double-stranded displacement at the single cleavage site. Our findings clarify the mechanism of Fz, establishing a foundation for engineering efforts. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45526.map.gz | 97.3 MB | EMDB map data format | |
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Header (meta data) | emd-45526-v30.xml emd-45526.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
Images | emd_45526.png | 52.6 KB | ||
Filedesc metadata | emd-45526.cif.gz | 7 KB | ||
Others | emd_45526_additional_1.map.gz emd_45526_half_map_1.map.gz emd_45526_half_map_2.map.gz | 51.3 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45526 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45526 | HTTPS FTP |
-Validation report
Summary document | emd_45526_validation.pdf.gz | 985.5 KB | Display | EMDB validaton report |
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Full document | emd_45526_full_validation.pdf.gz | 985.1 KB | Display | |
Data in XML | emd_45526_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_45526_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45526 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45526 | HTTPS FTP |
-Related structure data
Related structure data | 9cf1MC 9cerC 9cesC 9cetC 9ceuC 9cevC 9cewC 9cexC 9ceyC 9cezC 9cf0C 9cf2C 9cf3C 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_45526.map.gz / Format: CCP4 / Size: 103 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: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Ternary complex of PpFz1-omegaRNA-DNA
Entire | Name: Ternary complex of PpFz1-omegaRNA-DNA |
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Components |
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-Supramolecule #1: Ternary complex of PpFz1-omegaRNA-DNA
Supramolecule | Name: Ternary complex of PpFz1-omegaRNA-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Parasitella parasitica (fungus) |
-Macromolecule #1: Peptidyl-prolyl cis-trans isomerase
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 17.41167 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSQVYFDVEA DGQPIGRVVF KLYNDIVPKT AENFRALCTG EKGFGYAGSP FHRVIPDFML QGGDFTAGNG TGGKSIYGGK FPDENFKKH HDRPGLLSMA NAGPNTNGSQ FFITTVPCPW LDGKHVVFGE VVDGYDIVKK VESLGSPSGA TKARIVVAKS G EL UniProtKB: Peptidyl-prolyl cis-trans isomerase |
-Macromolecule #3: Maltose/maltodextrin-binding periplasmic protein,Parasitella para...
Macromolecule | Name: Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Parasitella parasitica (fungus) |
Molecular weight | Theoretical: 144.413969 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MKSSHHHHHH HHHHGSSMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN ...String: MKSSHHHHHH HHHHGSSMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKHMNADTDY SIAEAAFNKG ET AMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEAVNKDKPL GAV ALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTNS SSNNNNNNNN NNLG IEENL YFQSNAEAES DDDFQPPIIR RKRSSRENTQ QSGSQKRLKG KDKEIVADDN PILNTTTLDD YDYDDFQPPV VKRPD IGES SSSVNPTFFA AESSTRASHT SNNTPNTPSK RVITIKTTIK GIWKYDYRQP LYDLVHTTNL LVTHTYAFTK YIFLKE LAT DENFAFNELI TKDFFVEVFL SLVSAKAGNS ERLKDTTKRY RSLIGKHKDA YFEDAKYTPI SLAYAQQIAL YECAKVQ TA YFNNMKAHFG NRLRALINKL FKKKEKVESL TKEMEANNFS IKEIKQAIRK NVYQPCNQVK LAITKKNMPE SGLLDDKS V TQLNEFFSMY AVDYTFQKES IFYDVVANPE KHFKAFYKLA QLSEAYEVKP FACFPLRRTF IPCYMTVDSK ILNYHILKN KKVLKMDEKF NAWGRVVNLE RKAFKSQGCK KTLHFQGTLE TDGVGVSILK QNTDTNRKSV MPKKPLEDID DETKYIEKLE DAELKQTLG KCVLMDPGRR DLLYCMKETS RADKKEIMIF TKNDRSKCSR HFRRLRKLLQ PSQIREAETY LSGFATKSVN M EKFVEYIQ ARASVKDILY EYYGNETAKS ITEFYPESQF DFKVDQKCNL YYENLFVAKI RGFYPQPEHE PNDITLKSHM YH TYLQIML NQKHISERLN SEKRRKIEDL AKAILEQPHE SGHKTTISSL LGKLRLLPFR KMKFSTKLFS DNNDRKLVKN IKK KFGADA VLVLGNWSAP NTKYQDPTRN KGLRRMLKKN GFPLYLIDEF RTSSFCPKCE SDLEKFKVIP NPRPHNQEKQ PKVL CHGLL RCKNMSCLEQ QTSEGNQRLW NRDQAAVLNF RKILNCLRET KQRPPLFSRE PSKN UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Uncharacterized protein |
-Macromolecule #2: DNA non-target strand
Macromolecule | Name: DNA non-target strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.449246 KDa |
Sequence | String: (DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DA)(DA)(DA)(DC)(DA)(DT)(DC)(DC)(DA)(DG) (DC)(DA)(DA)(DA)(DC)(DA)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DT)(DT)(DC)(DA)(DA)(DA) (DA) (DA)(DC)(DT)(DA)(DA)(DT) ...String: (DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DA)(DA)(DA)(DC)(DA)(DT)(DC)(DC)(DA)(DG) (DC)(DA)(DA)(DA)(DC)(DA)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DT)(DT)(DC)(DA)(DA)(DA) (DA) (DA)(DC)(DT)(DA)(DA)(DT)(DT)(DT) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DC) |
-Macromolecule #4: DNA target strand
Macromolecule | Name: DNA target strand / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.675332 KDa |
Sequence | String: (DG)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DA) (DA)(DA)(DT)(DT)(DA)(DG)(DT)(DT)(DT)(DT) (DT)(DG)(DA)(DA)(DC)(DG)(DA)(DG)(DC) (DT)(DC)(DT)(DG)(DT)(DT)(DT)(DG)(DC)(DT) (DG) (DG)(DA)(DT)(DG)(DT)(DT) ...String: (DG)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DA) (DA)(DA)(DT)(DT)(DA)(DG)(DT)(DT)(DT)(DT) (DT)(DG)(DA)(DA)(DC)(DG)(DA)(DG)(DC) (DT)(DC)(DT)(DG)(DT)(DT)(DT)(DG)(DC)(DT) (DG) (DG)(DA)(DT)(DG)(DT)(DT)(DT)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DG)(DT)(DA) |
-Macromolecule #5: Parasitella parasitica Fanzor 1 omegaRNA
Macromolecule | Name: Parasitella parasitica Fanzor 1 omegaRNA / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: Parasitella parasitica (fungus) |
Molecular weight | Theoretical: 19.514656 KDa |
Sequence | String: UUAUCCACCA AAGUUAUCGC UUUGGUCAAU UAAUGCAGGU AAGCAACAUC CAGCAAACAG A |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.47 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14604 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |