+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33182 | |||||||||
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Title | CryoEM structure of type IV-A Csf-crRNA binary complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nuclease / STRUCTURAL PROTEIN-RNA COMPLEX | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zhang JT / Cui N / Huang HD / Jia N | |||||||||
Funding support | 1 items
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Citation | Journal: Mol.Cell / Year: 2023 Title: Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment Authors: Cui N / Zhang JT / Liu Y / Liu Y / Liu XY / Wang C / Huang H / Jia N | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33182.map.gz | 10.8 MB | EMDB map data format | |
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Header (meta data) | emd-33182-v30.xml emd-33182.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_33182.png | 66.8 KB | ||
Masks | emd_33182_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-33182.cif.gz | 5.8 KB | ||
Others | emd_33182_half_map_1.map.gz emd_33182_half_map_2.map.gz | 141.3 MB 141.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33182 | HTTPS FTP |
-Validation report
Summary document | emd_33182_validation.pdf.gz | 883.8 KB | Display | EMDB validaton report |
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Full document | emd_33182_full_validation.pdf.gz | 883.4 KB | Display | |
Data in XML | emd_33182_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_33182_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33182 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33182 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33182.map.gz / Format: CCP4 / Size: 178 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: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33182_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33182_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33182_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type IV-A Csf-crRNA binary complex
Entire | Name: Type IV-A Csf-crRNA binary complex |
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Components |
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-Supramolecule #1: Type IV-A Csf-crRNA binary complex
Supramolecule | Name: Type IV-A Csf-crRNA binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Supramolecule #2: Type IV-A Csf
Supramolecule | Name: Type IV-A Csf / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Supramolecule #3: crRNA
Supramolecule | Name: crRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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-Macromolecule #1: Csf1
Macromolecule | Name: Csf1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 28.675768 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HHHHHHHHHH MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLY GLSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR P EVVRKALS ...String: HHHHHHHHHH MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLY GLSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR P EVVRKALS IADRVNEGQK KWVTPVYFDR KAAAMGHGLI TRAGAEMLTQ EEQEFFQSVT PGERWALSYL MHSKRPEPEV GE CITEKVM TSLNKE |
-Macromolecule #2: Csf3
Macromolecule | Name: Csf3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 24.421953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVNLKVTIDL SNPMMEPGDL LHLDALLGAL RVSRARAEHG DAINPRDYHY DLPLERYQAP SGDWVFKASA FKLKRQLPNQ MWMQTGRLS IVEAARHRQS GYLQLRAGKP NPAGGPFKTS IYHRPIVQAE LTAFCVGDQQ GIEALLSECR QIGGKRGVGF G QVAGFKVE ...String: MVNLKVTIDL SNPMMEPGDL LHLDALLGAL RVSRARAEHG DAINPRDYHY DLPLERYQAP SGDWVFKASA FKLKRQLPNQ MWMQTGRLS IVEAARHRQS GYLQLRAGKP NPAGGPFKTS IYHRPIVQAE LTAFCVGDQQ GIEALLSECR QIGGKRGVGF G QVAGFKVE PVAETDCPWS WRALPADADP RLVTSEHARC IAAIRGPYWD RTLHVEALAP TP |
-Macromolecule #3: Csf2
Macromolecule | Name: Csf2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 37.322234 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIEVTVRNI TPIFSAAPGS NYITIDGTIN PPPGVSRFPL VRTRMMYVAA DVGDGVIKSV PLQIVPGNTM RSLLRRTMLK HVIEPALVE KGNKLSIGAY ATAYSGNATG NPDGVPSSFD EIATMRAHPF IGLFGGGPRM LEGRLMVDSL YPIHTNAERI L GAGYENEM ...String: MQIEVTVRNI TPIFSAAPGS NYITIDGTIN PPPGVSRFPL VRTRMMYVAA DVGDGVIKSV PLQIVPGNTM RSLLRRTMLK HVIEPALVE KGNKLSIGAY ATAYSGNATG NPDGVPSSFD EIATMRAHPF IGLFGGGPRM LEGRLMVDSL YPIHTNAERI L GAGYENEM MSGPITQVVW ARRMDPILNL GSSEDVEVIN GGAVAANGWI QDLLANSKAA ASKKKKAAAD EDESDGAAEE NG RGLKAFN AHEVVIPGLK WVWRISLDRP TDAQVGLVLL ALNKMTNERI AGGHSKDYGR FVIDGVSLNG EQVWSQSGIT GGE QYFDAV AEAIDGLSSK EFEQFAQSAK EA |
-Macromolecule #4: crRNA
Macromolecule | Name: crRNA / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 19.837855 KDa |
Sequence | String: GUGAACGGUG GAGCAACACC UGAAGGAAGG CUUGAUGAGC GUGUUCCCCG CAUACGCGGG G |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: 50.0 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: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25016 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |