+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37219 | |||||||||
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Title | Structure of AmCas12a with crRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CRISPR/Cas12a / DNA binding protein / DNA BINDING PROTEIN-RNA complex | |||||||||
Biological species | Anaeroglobus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Feng Y / Zhang X / Shi J / Ma P / Tang J / Huang X | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: A novel CRISPR/Cas12a in complex with a crRNA. Authors: Feng Y / Zhang X / Shi J / Ma P / Tang J / Huang X | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37219.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-37219-v30.xml emd-37219.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37219_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_37219.png | 73.1 KB | ||
Masks | emd_37219_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-37219.cif.gz | 6.6 KB | ||
Others | emd_37219_half_map_1.map.gz emd_37219_half_map_2.map.gz | 5.3 MB 5.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37219 | HTTPS FTP |
-Validation report
Summary document | emd_37219_validation.pdf.gz | 571 KB | Display | EMDB validaton report |
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Full document | emd_37219_full_validation.pdf.gz | 570.6 KB | Display | |
Data in XML | emd_37219_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_37219_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37219 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37219 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37219.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: 0.74 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37219_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of AmCas12a with crRNA
Entire | Name: Structure of AmCas12a with crRNA |
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Components |
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-Supramolecule #1: Structure of AmCas12a with crRNA
Supramolecule | Name: Structure of AmCas12a with crRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Anaeroglobus (bacteria) |
-Macromolecule #1: CRISPR-associated endonuclease Cas12a
Macromolecule | Name: CRISPR-associated endonuclease Cas12a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Anaeroglobus (bacteria) |
Molecular weight | Theoretical: 157.312344 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGPKKKRKVA AADYKDDDDK SRLEPGEKPY KCPECGKSFS QSGALTRHQR THTRMRTMVT FENFTKQYQV SKTLRFELIP QGKTLENMK RDGIISVDRQ RNDDYQKAKG ILDKLYKYIL DSTMETAVID WEELAIAIEE FRKSKDKKTY EKVQSKVRTA L LEHVKKQK ...String: MGPKKKRKVA AADYKDDDDK SRLEPGEKPY KCPECGKSFS QSGALTRHQR THTRMRTMVT FENFTKQYQV SKTLRFELIP QGKTLENMK RDGIISVDRQ RNDDYQKAKG ILDKLYKYIL DSTMETAVID WEELAIAIEE FRKSKDKKTY EKVQSKVRTA L LEHVKKQK VGTEDLFKGM FSSKIITGEV LAAFPEIRLS DEENLILEKF KDFTTYFTGF FENRKNVFTD EALSTSFTYR LV NDNFIKF FDNCTVMKNV VNISPDMAKS LETCVSDLGI FPGVSLEEVF SVSFYNRLLT QTGIDQFNQL LGGISGKEGE YKK QGLNEI INLAMQQSPE VKEVLKNKAH RFTPLFKQIL SDRSTMSFIP DAFADDDEVL SAVDAYRKYL LEKNIGDRAF QLIS DIEEY SPELMRIGGK YVSVLSQLLF NSWSEIRDGV KAYKESLITG KKTKKELENI DKGIKYGVTL QEIKEALPKK DIYEE VKKY AMSVVKDYHA GLAEPLPEKI ETDDERASIK HIMDSMLGLY RFLEYFSHDS IEDTDPVFGE CLDTILDDMN ETVPLY NKV RNFSTRKVYS TEKFKLNFNN SSLANGWDKN KEQANGAVLL KKAGEYFLGI FNSKNKPKLV SDGGGGTGYE KMIYKQF PD FKKMLPKCTI SRKETKAHFQ KSDEDFTLLT DKFEKSLVIT KKIYDLGTQT VNGKKKFQVD YPRLTGDMEG YRAALKEW I DFGKKFIQAY ASTAIYDTSL FRNSSDYPDL PSFYKDVDNI CYKLTFECIP DAVINDCIDD GSLYLFKLHN KDFSAGSIG KPNLHTLYWK AIFEEENLSD VVVKLNGQAE LFYRPKSLTR PVVHEAGEVI INKTTSTGLP VPDDVYVELS KFVRNGKKGN LTDKAKNWL DKVTVRKTPH AIIKDRRFTV DKFFFHVPIT LNYKADSSPY RFNDFVRQYV KDCSDVNIIG IDRGERNLIY A VVIDGKGN IIEQRSFNTV GTYNYQEKLE QKEKERQTAR QDWATVTKIK DLKKGYLSAV VHELSKMIVK YKAIVVLENL NV GFKRMRG GIAERSVYQQ FEKALIDKLN YLVFKDEEQS GYGGVLNAYQ LTDKFESFSK MGQQTGFLFY VPAAYTSKID PLT GFINPF SWKHVKNRED RRNFLNLFSK LYYDVNTHDF VLAYHHSNKD SKYTIKGNWE IADWDILIQE NKEVFGKTGT PYCV GKRIV YMDDSTTGHN RMCAYYPHTE LKKLLSEYGI EYTSGQDLLK IIQEFDDDKL VKGLFYIIKA ALQMRNSNSE TGEDY ISSP IEGRPGICFD SRAEADTLPH NADANGAFHI AMKGLLLTER IRNDDKLAIS NEEWLNYIQE MRGASLVPRG SHHHHH HHH HH |
-Macromolecule #2: RNA (44-MER)
Macromolecule | Name: RNA (44-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Anaeroglobus (bacteria) |
Molecular weight | Theoretical: 14.125415 KDa |
Sequence | String: UAAUUUCUAC UAAGUGUAGA UGACAUAUGG AAAACGAACU AUGU |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / 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
Buffer | pH: 7.5 |
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Grid | Material: NICKEL/TITANIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.63 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8kgf: |