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- EMDB-45527: Parasitella parasitica Fanzor (PpFz) State 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-45527
TitleParasitella parasitica Fanzor (PpFz) State 3
Map data
Sample
  • Complex: Ternary complex of PpFz1-omegaRNA-DNA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • DNA: DNA non-target strand
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1
    • DNA: DNA target strand
    • RNA: Parasitella parasitica Fanzor 1 omegaRNA
    • DNA: DNA substrate model
    • DNA: DNA substrate model
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsFanzor / 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 / carbohydrate transmembrane transporter activity / maltose binding ...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 / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / peptidyl-prolyl cis-trans isomerase activity / cellular response to starvation / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / cell chemotaxis / peptidylprolyl isomerase / mitochondrial intermembrane space / protein transport / protein folding / outer membrane-bounded periplasmic space / periplasmic space / mRNA binding / DNA damage response / mitochondrion / nucleus / membrane / cytoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Uncharacterized protein / Maltose/maltodextrin-binding periplasmic protein / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesParasitella parasitica (fungus) / Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsXu P / Saito M / Zhang F
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionJun 27, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45527.png

Downloads & links

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Map

FileDownload / File: emd_45527.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.018832138 - 2.128856
Average (Standard dev.)0.0016839744 (±0.030087018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ternary complex of PpFz1-omegaRNA-DNA

EntireName: Ternary complex of PpFz1-omegaRNA-DNA
Components
  • Complex: Ternary complex of PpFz1-omegaRNA-DNA
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • DNA: DNA non-target strand
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1
    • DNA: DNA target strand
    • RNA: Parasitella parasitica Fanzor 1 omegaRNA
    • DNA: DNA substrate model
    • DNA: DNA substrate model
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ternary complex of PpFz1-omegaRNA-DNA

SupramoleculeName: Ternary complex of PpFz1-omegaRNA-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Parasitella parasitica (fungus)

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.41167 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSQVYFDVEA DGQPIGRVVF KLYNDIVPKT AENFRALCTG EKGFGYAGSP FHRVIPDFML QGGDFTAGNG TGGKSIYGGK FPDENFKKH HDRPGLLSMA NAGPNTNGSQ FFITTVPCPW LDGKHVVFGE VVDGYDIVKK VESLGSPSGA TKARIVVAKS G EL

UniProtKB: Peptidyl-prolyl cis-trans isomerase

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Macromolecule #3: Maltose/maltodextrin-binding periplasmic protein,Parasitella para...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Parasitella parasitica (fungus)
Molecular weightTheoretical: 144.413969 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

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Macromolecule #2: DNA non-target strand

MacromoleculeName: DNA non-target strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.449246 KDa
SequenceString: (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)

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Macromolecule #4: DNA target strand

MacromoleculeName: DNA target strand / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.675332 KDa
SequenceString: (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)

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Macromolecule #6: DNA substrate model

MacromoleculeName: DNA substrate model / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.400317 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)

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Macromolecule #7: DNA substrate model

MacromoleculeName: DNA substrate model / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.605356 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

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Macromolecule #5: Parasitella parasitica Fanzor 1 omegaRNA

MacromoleculeName: Parasitella parasitica Fanzor 1 omegaRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Parasitella parasitica (fungus)
Molecular weightTheoretical: 19.514656 KDa
SequenceString:
UUAUCCACCA AAGUUAUCGC UUUGGUCAAU UAAUGCAGGU AAGCAACAUC CAGCAAACAG A

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / 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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.47 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18003
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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