+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36123 | |||||||||
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Title | Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | a protein complex / VIRAL PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Neisseria meningitidis (bacteria) / Haemophilus parainfluenzae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
Authors | Yin H / Li Z / Yu GM / Li XZ | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex Authors: Yin H / Li Z / Yu GM / Li XZ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36123.map.gz | 78.7 MB | EMDB map data format | |
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Header (meta data) | emd-36123-v30.xml emd-36123.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36123_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_36123.png | 94.1 KB | ||
Filedesc metadata | emd-36123.cif.gz | 5.9 KB | ||
Others | emd_36123_half_map_1.map.gz emd_36123_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36123 | HTTPS FTP |
-Validation report
Summary document | emd_36123_validation.pdf.gz | 835.4 KB | Display | EMDB validaton report |
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Full document | emd_36123_full_validation.pdf.gz | 835 KB | Display | |
Data in XML | emd_36123_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | emd_36123_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36123 | HTTPS FTP |
-Related structure data
Related structure data | 8ja0MC 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_36123.map.gz / Format: CCP4 / Size: 83.7 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: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36123_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36123_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : a protein complex
Entire | Name: a protein complex |
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Components |
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-Supramolecule #1: a protein complex
Supramolecule | Name: a protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Neisseria meningitidis (bacteria) |
-Macromolecule #1: CRISPR-associated endonuclease Cas9
Macromolecule | Name: CRISPR-associated endonuclease Cas9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Neisseria meningitidis (bacteria) |
Molecular weight | Theoretical: 124.613883 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAAFKPNSIN YILGLDIGIA SVGWAMVEID EEENPIRLID LGVRVFERAE VPKTGDSLAM ARRLARSVRR LTRRRAHRLL RTRRLLKRE GVLQAANFDE NGLIKSLPNT PWQLRAAALD RKLTPLEWSA VLLHLIKHRG YLSQRKNEGE TADKELGALL K GVAGNAHA ...String: MAAFKPNSIN YILGLDIGIA SVGWAMVEID EEENPIRLID LGVRVFERAE VPKTGDSLAM ARRLARSVRR LTRRRAHRLL RTRRLLKRE GVLQAANFDE NGLIKSLPNT PWQLRAAALD RKLTPLEWSA VLLHLIKHRG YLSQRKNEGE TADKELGALL K GVAGNAHA LQTGDFRTPA ELALNKFEKE SGHIRNQRSD YSHTFSRKDL QAELILLFEK QKEFGNPHVS GGLKEGIETL LM TQRPALS GDAVQKMLGH CTFEPAEPKA AKNTYTAERF IWLTKLNNLR ILEQGSERPL TDTERATLMD EPYRKSKLTY AQA RKLLGL EDTAFFKGLR YGKDNAEAST LMEMKAYHAI SRALEKEGLK DKKSPLNLSP ELQDEIGTAF SLFKTDEDIT GRLK DRIQP EILEALLKHI SFDKFVQISL KALRRIVPLM EQGKRYDEAC AEIYGDHYGK KNTEEKIYLP PIPADEIRNP VVLRA LSQA RKVINGVVRR YGSPARIHIE TAREVGKSFK DRKEIEKRQE ENRKDREKAA AKFREYFPNF VGEPKSKDIL KLRLYE QQH GKCLYSGKEI NLGRLNEKGY VEIDHALPFS RTWDDSFNNK VLVLGSENQN KGNQTPYEYF NGKDNSREWQ EFKARVE TS RFPRSKKQRI LLQKFDEDGF KERNLNDTRY VNRFLCQFVA DRMRLTGKGK KRVFASNGQI TNLLRGFWGL RKVRAEND R HHALDAVVVA CSTVAMQQKI TRFVRYKEMN AFDGKTIDKE TGEVLHQKTH FPQPWEFFAQ EVMIRVFGKP DGKPEFEEA DTLEKLRTLL AEKLSSRPEA VHEYVTPLFV SRAPNRKMSG QGHMETVKSA KRLDEGVSVL RVPLTQLKLK DLEKMVNRER EPKLYEALK ARLEAHKDDP AKAFAEPFYK YDKAGNRTQQ VKAVRVEQVQ KTGVWVRNHN GIADNATMVR VDVFEKGDKY Y LVPIYSWQ VAKGILPDRA VVQGKDEEDW QLIDDSFNFK FSLHPNDLVE VITKKARMFG YFASCHRGTG NINIRIHDLD HK IGKNGIL EGIGVKTALS FQKYQIDELG KEIRPCRLKK RPPVR UniProtKB: CRISPR-associated endonuclease Cas9 |
-Macromolecule #2: Uncharacterized protein
Macromolecule | Name: Uncharacterized protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haemophilus parainfluenzae (bacteria) |
Molecular weight | Theoretical: 9.985316 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKITSSNFAT IATSENFAKL SVLPKNHREP IKGLFKSAVE QFSSARDFFK NENYSKELAE KFNKEAVNEA VEKLQKAIDL AEKQGIQF UniProtKB: Uncharacterized protein |
-Macromolecule #3: RNA (117-MER)
Macromolecule | Name: RNA (117-MER) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Neisseria meningitidis (bacteria) |
Molecular weight | Theoretical: 37.367059 KDa |
Sequence | String: UAACUUUACG UUGUAGCUCC CUUUCUCGAA AGAGAACCGU UGCUACAAUA AGGCCGUCUG AAAAGAUGUG CCGCAACGCU CUGCCCCUU AAAGCUCCUG CUUUAAGGGG CAUCGUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |