+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18692 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Apo ReChb , Rec1 improved | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Cas / BIOSYNTHETIC PROTEIN / cryo-EM / ancestral sequence reconstruction / biotechnology | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Lopez-Alonso JP / Tascon I / Ubarretxena-Belandia I | |||||||||
Funding support | 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_18692.map.gz | 118 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-18692-v30.xml emd-18692.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18692_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_18692.png | 125.1 KB | ||
Masks | emd_18692_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-18692.cif.gz | 6.1 KB | ||
Others | emd_18692_half_map_1.map.gz emd_18692_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18692 | HTTPS FTP |
-Validation report
Summary document | emd_18692_validation.pdf.gz | 962.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_18692_full_validation.pdf.gz | 962.4 KB | Display | |
Data in XML | emd_18692_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_18692_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18692 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_18692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8238 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_18692_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_18692_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_18692_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : apo ReChb
Entire | Name: apo ReChb |
---|---|
Components |
|
-Supramolecule #1: apo ReChb
Supramolecule | Name: apo ReChb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: ReChb
Macromolecule | Name: ReChb / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GPKMFSNFTN QYPLSKTLRF ELKPVGKTLE HIEKKGLLEQ DEKRAEDYKK VKKIIDEYHK DFIEEALNNV KLNGEGLEEY YELYFKKNKD DKDKKKKEFE KIQDNLRKQI VEAFKNHEKY KNLFKKELIK EDLPNWLKNS EDTGEEDKET VEKFKNFTTY FTGFHENRKN ...String: GPKMFSNFTN QYPLSKTLRF ELKPVGKTLE HIEKKGLLEQ DEKRAEDYKK VKKIIDEYHK DFIEEALNNV KLNGEGLEEY YELYFKKNKD DKDKKKKEFE KIQDNLRKQI VEAFKNHEKY KNLFKKELIK EDLPNWLKNS EDTGEEDKET VEKFKNFTTY FTGFHENRKN MYSDEEKSTA IAYRLIHENL PKFLDNMKVF EKIKEKHPEA EQLEKTLKDL GEEEVLGGNN VEDIFSLDYF NHTLTQSGID IYNTIIGGKT EEDGNKKIQG LNEYINLYRQ KNNEKNRKLP KLKPLYKQIL SDRESLSFIP EAFENDEELL EAIEEFYENL NFSNNNEATN VLEKLKELLS NLADYDLNKI YIRNDTSLTD ISQKIFGDWS VIKDALNAHY DQTYPKKKKK KSKEKLEEKR EKWLKKQKYF SIAELQEALD SYCKESDESK EQKENSIADY FKTLAQTKNE TDKKTDLIEN IKSKYQYPND KKLAQDKEFK DVEKIKAFLD SIMNLQHFVK PLHLVKGGSA GAEMEKDEAF YSEFEALYEE LSQVIPLYNK VRNYLTQKPY STEKIKLNFE NSTLLDGWDV NKETDNTSVL LRKDGLYYLG IMNKKHNKVF ENIPESNEND KCYEKMDYKL LPGANKMLPK VFFSNKNIDY FNPSAEILEI YENGTHKKSG DNFNLDDCHK LIDFFKESIN KHEDWKKFGF KFSPTSSYED ISGFYREVEQ QGYKISFKNI SESYIDELVD EGKLYLFQIY NKDFSPYSKG KPNLHTLYWK ALFDEENLKD VVYKLNGEAE VFYRKASINE TIVHKANEPI KNKNPLNPKK QSTFEYDIIK DRRYTVDKFQ FHVPITMNFK AEGNSNINDE VNEFLKGNAP DVNIIGIDRG ERHLLYLTLI DQKGKIVEQD SLNTITNEHN ETDYHALLDD KEKERDKARK SWGTIENIKE LKEGYLSQVV HKIAKLMVEH NAIVVMEDLN FGFKRGRFKV EKQVYQKFEK MLIDKLNYLV DKDKEPNEPG GLLNAYQLTN KFESFQKMGK QSGFLFYVPA WNTSKIDPTT GFVNLFHPRY ENVEKAKEFF NKFDSIRYNS EKDYFEFAFD YNNFTEKAEG TKWTVCTYGE RIKTYRNADK NNQWDSKEVN VTEEFKNLFD EYNIDYKNGN DLKEAILSQD DADFFKSLLH LLRLTLQMRN SITGTEIDYI ISPVANENGE FFDSRKADES LPKDADANGA YHIARKGLWV LEQIKQTDDL KKVNLAISNK EWLEFVQERK N |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: 14874 / Average exposure time: 2.1 sec. / Average electron dose: 49.8 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 |