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Yorodumi- EMDB-31829: Cryo-EM structure of E.coli retron-Ec86 in complex with its effec... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31829 | |||||||||
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Title | Cryo-EM structure of E.coli retron-Ec86 in complex with its effector at 2.8 angstrom | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Reverse transcriptase / RNA BINDING PROTEIN / TRANSFERASE-RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | Function and homology information RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||
Authors | Wang YJ / Guan ZY | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Structural insight into anti-phage Retron-Ec86 complex Authors: Wang TJ / Guan ZY / Zou TT | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31829.map.gz | 79 MB | EMDB map data format | |
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Header (meta data) | emd-31829-v30.xml emd-31829.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_31829.png | 171.9 KB | ||
Filedesc metadata | emd-31829.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31829 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31829 | HTTPS FTP |
-Validation report
Summary document | emd_31829_validation.pdf.gz | 517.5 KB | Display | EMDB validaton report |
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Full document | emd_31829_full_validation.pdf.gz | 517.1 KB | Display | |
Data in XML | emd_31829_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_31829_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31829 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31829 | HTTPS FTP |
-Related structure data
Related structure data | 7v9xMC 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_31829.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
-Sample components
-Entire : retron-Ec86 (RT-msDNA-RNA)
Entire | Name: retron-Ec86 (RT-msDNA-RNA) |
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Components |
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-Supramolecule #1: retron-Ec86 (RT-msDNA-RNA)
Supramolecule | Name: retron-Ec86 (RT-msDNA-RNA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RNA-directed DNA polymerase from retron EC86
Macromolecule | Name: RNA-directed DNA polymerase from retron EC86 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 37.83207 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKSAEYLNTF RLRNLGLPVM NNLHDMSKAT RISVETLRLL IYTADFRYRI YTVEKKGPEK RMRTIYQPSR ELKALQGWVL RNILDKLSS SPFSIGFEKH QSILNNATPH IGANFILNID LEDFFPSLTA NKVFGVFHSL GYNRLISSVL TKICCYKNLL P QGAPSSPK ...String: MKSAEYLNTF RLRNLGLPVM NNLHDMSKAT RISVETLRLL IYTADFRYRI YTVEKKGPEK RMRTIYQPSR ELKALQGWVL RNILDKLSS SPFSIGFEKH QSILNNATPH IGANFILNID LEDFFPSLTA NKVFGVFHSL GYNRLISSVL TKICCYKNLL P QGAPSSPK LANLICSKLD YRIQGYAGSR GLIYTRYADD LTLSAQSMKK VVKARDFLFS IIPSEGLVIN SKKTCISGPR SQ RKVTGLV ISQEKVGIGR EKYKEIRAKI HHIFCGKSSE IEHVRGWLSF ILSVDSKSHR RLITYISKLE KKYGKNPLNK AKT LEHHHH HHHH UniProtKB: Retron Ec86 reverse transcriptase |
-Macromolecule #2: retron St85 family effector protein
Macromolecule | Name: retron St85 family effector protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 35.538242 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNKKFTDEQQ QQLIGHLTKK GFYRGANIKI TIFLCGGDVA NHQSWRHQLS QFLAKFSDVD IFYPEDLFDD LLAGQGQHSL LSLENILAE AVDVIILFPE SPGSFTELGA FSNNENLRRK LICIQDAKFK SKRSFINYGP VRLLRKFNSK SVLRCSSNEL K EMCDSSID ...String: MNKKFTDEQQ QQLIGHLTKK GFYRGANIKI TIFLCGGDVA NHQSWRHQLS QFLAKFSDVD IFYPEDLFDD LLAGQGQHSL LSLENILAE AVDVIILFPE SPGSFTELGA FSNNENLRRK LICIQDAKFK SKRSFINYGP VRLLRKFNSK SVLRCSSNEL K EMCDSSID VARKLRLYKK LMASIKKVRK ENKVSKDIGN ILYAERFLLP CIYLLDSVNY RTLCELAFKA IKQDDVLSKI IV RSVVSRL INERKILQMT DGYQVTALGA SYVRSVFDRK TLDRLRLEIM NFENRRKSTF NYDKIPYAHP UniProtKB: UNIPROTKB: A0A7A0NNW9 |
-Macromolecule #3: DNA (105-MER)
Macromolecule | Name: DNA (105-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 32.468803 KDa |
Sequence | String: (DG)(DA)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DG) (DC)(DA)(DC)(DC)(DC)(DT)(DT)(DA)(DC)(DG) (DT)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA) (DA)(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DC)(DC) (DT) (DG)(DG)(DT)(DT)(DG)(DG) ...String: (DG)(DA)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DG) (DC)(DA)(DC)(DC)(DC)(DT)(DT)(DA)(DC)(DG) (DT)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA) (DA)(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DC)(DC) (DT) (DG)(DG)(DT)(DT)(DG)(DG)(DC)(DT) (DC)(DG)(DG)(DA)(DG)(DA)(DG)(DC)(DA)(DT) (DC)(DA) (DG)(DG)(DC)(DG)(DA)(DT)(DG) (DC)(DT)(DC)(DT)(DC)(DC)(DG)(DT)(DT)(DC) (DC)(DA)(DA) (DC)(DA)(DA)(DG)(DG)(DA) (DA)(DA)(DA)(DC)(DA)(DG)(DA)(DC)(DA)(DG) (DT)(DA)(DA)(DC) (DT)(DC)(DA)(DG)(DA) GENBANK: GENBANK: M24408.1 |
-Macromolecule #4: RNA (81-MER)
Macromolecule | Name: RNA (81-MER) / type: rna / ID: 4 / Number of copies: 2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 25.870203 KDa |
Sequence | String: UGCGCACCCU UAGCGAGAGG UUUAUCAUUA AGGUCAACCU CUGGAUGUUG UUUCGGCAUC CUGCAUUGAA UCUGAGUUAC U GENBANK: GENBANK: M24408.1 |
-Macromolecule #5: RNA (14-MER)
Macromolecule | Name: RNA (14-MER) / type: rna / ID: 5 / Number of copies: 2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 4.541771 KDa |
Sequence | String: CGUAAGGGUG CGCA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 8 |
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: 53.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: RANDOM CONICAL TILT |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137409 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) |