+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18693 | |||||||||
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Title | Ternary complex of ReChb - crRNA - target dsDNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cas / BIOSYNTHETIC PROTEIN / cryo-EM / ancestral sequence reconstruction / biotechnology / DNA / RNA | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||
Authors | Lopez-Alonso JP / Ubarretxena-Belandia I / Tascon I | |||||||||
Funding support | 1 items
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Citation | Journal: Nature Biotechnology / Year: 2024 Title: A resurrected ancestor of Cas12a expands target access and substrate 2 recognition for nucleic-acid editing and detection Authors: Jabalera Y / Tascon I / Samperio S / Lopez-Alonso JP / Gonzalez-Lopez M / Aransay AM / Abascal-Palacios G / Beisel CL / Ubarretxena-Belandia I / Jimenez-Perez R | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18693.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-18693-v30.xml emd-18693.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18693_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_18693.png | 96.8 KB | ||
Masks | emd_18693_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-18693.cif.gz | 7.5 KB | ||
Others | emd_18693_half_map_1.map.gz emd_18693_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18693 | HTTPS FTP |
-Validation report
Summary document | emd_18693_validation.pdf.gz | 971 KB | Display | EMDB validaton report |
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Full document | emd_18693_full_validation.pdf.gz | 970.6 KB | Display | |
Data in XML | emd_18693_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_18693_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18693 | HTTPS FTP |
-Related structure data
Related structure data | 8qweMC 8qwdC 8qwfC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18693.map.gz / Format: CCP4 / Size: 125 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: 0.8238 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18693_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18693_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18693_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of ReChb - crRNA - target dsDNA
Entire | Name: Ternary complex of ReChb - crRNA - target dsDNA |
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Components |
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-Supramolecule #1: Ternary complex of ReChb - crRNA - target dsDNA
Supramolecule | Name: Ternary complex of ReChb - crRNA - target dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: ReChb
Macromolecule | Name: ReChb / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 148.954109 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GPKMFSNFTN QYPLSKTLRF ELKPVGKTLE HIEKKGLLEQ DEKRAEDYKK VKKIIDEYHK DFIEEALNNV KLNGEGLEEY YELYFKKNK DDKDKKKKEF EKIQDNLRKQ IVEAFKNHEK YKNLFKKELI KEDLPNWLKN SEDTGEEDKE TVEKFKNFTT Y FTGFHENR ...String: GPKMFSNFTN QYPLSKTLRF ELKPVGKTLE HIEKKGLLEQ DEKRAEDYKK VKKIIDEYHK DFIEEALNNV KLNGEGLEEY YELYFKKNK DDKDKKKKEF EKIQDNLRKQ IVEAFKNHEK YKNLFKKELI KEDLPNWLKN SEDTGEEDKE TVEKFKNFTT Y FTGFHENR KNMYSDEEKS TAIAYRLIHE NLPKFLDNMK VFEKIKEKHP EAEQLEKTLK DLGEEEVLGG NNVEDIFSLD YF NHTLTQS GIDIYNTIIG GKTEEDGNKK IQGLNEYINL YRQKNNEKNR KLPKLKPLYK QILSDRESLS FIPEAFENDE ELL EAIEEF YENLNFSNNN EATNVLEKLK ELLSNLADYD LNKIYIRNDT SLTDISQKIF GDWSVIKDAL NAHYDQTYPK KKKK KSKEK LEEKREKWLK KQKYFSIAEL QEALDSYCKE SDESKEQKEN SIADYFKTLA QTKNETDKKT DLIENIKSKY QYPND KKLA QDKEFKDVEK IKAFLDSIMN LQHFVKPLHL VKGGSAGAEM EKDEAFYSEF EALYEELSQV IPLYNKVRNY LTQKPY STE KIKLNFENST LLDGWDVNKE TDNTSVLLRK DGLYYLGIMN KKHNKVFENI PESNENDKCY EKMDYKLLPG ANKMLPK VF FSNKNIDYFN PSAEILEIYE NGTHKKSGDN FNLDDCHKLI DFFKESINKH EDWKKFGFKF SPTSSYEDIS GFYREVEQ Q GYKISFKNIS ESYIDELVDE GKLYLFQIYN KDFSPYSKGK PNLHTLYWKA LFDEENLKDV VYKLNGEAEV FYRKASINE TIVHKANEPI KNKNPLNPKK QSTFEYDIIK DRRYTVDKFQ FHVPITMNFK AEGNSNINDE VNEFLKGNAP DVNIIGIDRG ERHLLYLTL IDQKGKIVEQ DSLNTITNEH NETDYHALLD DKEKERDKAR KSWGTIENIK ELKEGYLSQV VHKIAKLMVE H NAIVVMED LNFGFKRGRF KVEKQVYQKF EKMLIDKLNY LVDKDKEPNE PGGLLNAYQL TNKFESFQKM GKQSGFLFYV PA WNTSKID PTTGFVNLFH PRYENVEKAK EFFNKFDSIR YNSEKDYFEF AFDYNNFTEK AEGTKWTVCT YGERIKTYRN ADK NNQWDS KEVNVTEEFK NLFDEYNIDY KNGNDLKEAI LSQDDADFFK SLLHLLRLTL QMRNSITGTE IDYIISPVAN ENGE FFDSR KADESLPKDA DANGAYHIAR KGLWVLEQIK QTDDLKKVNL AISNKEWLEF VQERKN |
-Macromolecule #2: crRNA
Macromolecule | Name: crRNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12.696498 KDa |
Sequence | String: GAAUUUCUAC UGUUGUAGAU UCCUAAGGCG UUACCCCAAU |
-Macromolecule #3: target DNA
Macromolecule | Name: target DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 11.983707 KDa |
Sequence | String: (DC)(DC)(DC)(DT)(DC)(DC)(DC)(DA)(DT)(DT) (DG)(DG)(DG)(DG)(DT)(DA)(DA)(DC)(DG)(DC) (DC)(DT)(DT)(DA)(DG)(DG)(DA)(DT)(DA) (DA)(DA)(DT)(DA)(DT)(DG)(DC)(DT)(DA)(DG) |
-Macromolecule #4: non target DNA
Macromolecule | Name: non target DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12.023731 KDa |
Sequence | String: (DC)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DT)(DT) (DT)(DA)(DT)(DC)(DC)(DT)(DA)(DA)(DG)(DG) (DC)(DG)(DT)(DT)(DA)(DC)(DC)(DC)(DC) (DA)(DA)(DT)(DG)(DG)(DG)(DA)(DG)(DG)(DG) |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / 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
Concentration | 2.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 17896 / Average exposure time: 2.12 sec. / Average electron dose: 50.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: other / Details: ModelAngelo |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8qwe: |