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Yorodumi- EMDB-33039: Cryo-EM structure of a Group II Intron Complexed with its Reverse... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33039 | |||||||||
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Title | Cryo-EM structure of a Group II Intron Complexed with its Reverse Transcriptase | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information intron homing / mRNA processing / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | |||||||||
Biological species | Lactococcus cremoris (lactic acid bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Liu N / Dong XL / Qu GS / Wang J / Wang HW / Belfort M | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Functionalized graphene grids with various charges for single-particle cryo-EM Authors: Lu Y / Liu N / Liu Y / Zheng L / Yang J / Wang J / Jia X / Zi Q / Peng H / Rao Y / Wang HW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33039.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-33039-v30.xml emd-33039.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_33039.png | 79 KB | ||
Masks | emd_33039_msk_1.map | 64 MB | Mask map | |
Others | emd_33039_half_map_1.map.gz emd_33039_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33039 | HTTPS FTP |
-Validation report
Summary document | emd_33039_validation.pdf.gz | 733.7 KB | Display | EMDB validaton report |
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Full document | emd_33039_full_validation.pdf.gz | 733.2 KB | Display | |
Data in XML | emd_33039_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_33039_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33039 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33039 | HTTPS FTP |
-Related structure data
Related structure data | 8h2hM M: atomic model generated by this map |
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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_33039.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33039_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33039_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33039_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of a spliced group II intron RNP
Entire | Name: Cryo-EM structure of a spliced group II intron RNP |
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Components |
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-Supramolecule #1: Cryo-EM structure of a spliced group II intron RNP
Supramolecule | Name: Cryo-EM structure of a spliced group II intron RNP / type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Lactococcus cremoris (lactic acid bacteria) |
-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 | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (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: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399660 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |