+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36831 | |||||||||
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Title | ICP1 Csy-dsDNA complex (form 1) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | IMMUNE SYSTEM-RNA-DNA complex / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vibrio phage ICP1_2004_A (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Zhang LX / Feng Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure of csy complex with long DNA State1 Authors: Zhang LX / Feng Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36831.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-36831-v30.xml emd-36831.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36831_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_36831.png | 36.6 KB | ||
Filedesc metadata | emd-36831.cif.gz | 6 KB | ||
Others | emd_36831_half_map_1.map.gz emd_36831_half_map_2.map.gz | 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36831 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36831 | HTTPS FTP |
-Validation report
Summary document | emd_36831_validation.pdf.gz | 865.4 KB | Display | EMDB validaton report |
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Full document | emd_36831_full_validation.pdf.gz | 865 KB | Display | |
Data in XML | emd_36831_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_36831_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36831 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36831 | HTTPS FTP |
-Related structure data
Related structure data | 8k28MC 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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-Map
File | Download / File: emd_36831.map.gz / Format: CCP4 / Size: 52.7 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36831_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36831_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : csy complex
Entire | Name: csy complex |
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Components |
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-Supramolecule #1: csy complex
Supramolecule | Name: csy complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
-Macromolecule #1: Csy1
Macromolecule | Name: Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 20.409918 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIKEMIEDFI SKGGLIFTHS GRYTNTNNSC FIFNKNDIGV DTKVDMYTPK SAGIKNEEGE NLWQVLNKAN MFYRIYSGEL GEELQYLLK SCCTAKEDVT TLPQIYFKNG EGYDILVPIG NAHNLISGTE YLWEHKYYNT FTQKLGGSNP QNCTHACNKM R GGFKQFNC TPPQVEDNYN A UniProtKB: Csy1 |
-Macromolecule #2: Csy2
Macromolecule | Name: Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 27.401547 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRKFIIVKNV KVDGINAKSS DITVGMPPAT TFCGLGETMS IKTGIVVKAV SYGSVKFEVR GSRFNTSVTK FAWQDRGNGG KANNNSPIQ PKPLADGVFT LCFEVEWEDC AEVLVDKVTN FINTARIAGG TIASFNKPFV KVAKDAEELA SVKNAMMPCY V VVDCGVEV ...String: MRKFIIVKNV KVDGINAKSS DITVGMPPAT TFCGLGETMS IKTGIVVKAV SYGSVKFEVR GSRFNTSVTK FAWQDRGNGG KANNNSPIQ PKPLADGVFT LCFEVEWEDC AEVLVDKVTN FINTARIAGG TIASFNKPFV KVAKDAEELA SVKNAMMPCY V VVDCGVEV NIFEDAVNRK LQPMVNGYKK LEKIVDNKHM RDKFTPAYLA TPTYTMIGYK MVSNVDNFDQ ALWQYGENTK VK TIGGIYN D UniProtKB: Csy2 |
-Macromolecule #3: Csy3
Macromolecule | Name: Csy3 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 33.399301 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTKLKAPAVL AYSRKINPTN ALMFAVNWSD RDNTTAVMVG TKTVAGTQSV RGNPNDADKG NIQTVNFANL PHNKNTLLVK YNVKFVGDV FKAELGGGEY SNTLQTALEN TDFGTLAYRY VYNIAAGRTL WRNRVGAESI ETVITVNDQT FTFSDLLVNE F DEDVDVAE ...String: MTKLKAPAVL AYSRKINPTN ALMFAVNWSD RDNTTAVMVG TKTVAGTQSV RGNPNDADKG NIQTVNFANL PHNKNTLLVK YNVKFVGDV FKAELGGGEY SNTLQTALEN TDFGTLAYRY VYNIAAGRTL WRNRVGAESI ETVITVNDQT FTFSDLLVNE F DEDVDVAE IADMVAGVLS GEGFVTLKVE HYMLLGEGSE VFPSQEFVEN SKLSKQLFDL NGQAAMHDQK IGNAIRTIDT WY EDATTPI AVEPYGSVVR NGVAYRAGNK TDLFTLMDGA VNGKSLTEED QMFVTANLIR GGVFGGGKD UniProtKB: Csy3 |
-Macromolecule #4: Csy4
Macromolecule | Name: Csy4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 18.73668 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MYNTISITVV DADDVGVNFV VSKVLSTLHN KGIFNGEVGV TFPRMDKNVG DIITLFSKTG VDRKVLTSTL NTLTDFIHIG KPKEADKVK TYRKVDTKSK GKLIRRCIKR KGVSAETAES LYGNYKGEKC KLPYIVVNSK STGQRFSMFL EECENSEKFN S YGLCIVSC UniProtKB: Csy4 |
-Macromolecule #5: DNA (33-MER)
Macromolecule | Name: DNA (33-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 10.154547 KDa |
Sequence | String: (DT)(DA)(DA)(DG)(DC)(DA)(DA)(DA)(DG)(DG) (DG)(DT)(DT)(DG)(DA)(DC)(DG)(DA)(DA)(DA) (DG)(DC)(DC)(DC)(DT)(DT)(DT)(DG)(DT) (DC)(DC)(DC)(DT) |
-Macromolecule #6: DNA (27-MER)
Macromolecule | Name: DNA (27-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 8.330393 KDa |
Sequence | String: (DA)(DG)(DG)(DG)(DA)(DC)(DA)(DA)(DA)(DG) (DG)(DG)(DC)(DT)(DT)(DT)(DC)(DC)(DA)(DT) (DT)(DT)(DA)(DT)(DT)(DT)(DA) |
-Macromolecule #7: RNA (59-MER)
Macromolecule | Name: RNA (59-MER) / type: rna / ID: 7 / Number of copies: 1 |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 18.701021 KDa |
Sequence | String: CUUAAAGAGU CAACCCUUUG CUUAUCUUCC CUAUUUAAAU GUUAGCAGCC GCAUAGGCU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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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: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |