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Yorodumi- EMDB-34398: Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34398 | |||||||||
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Title | Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cryo-EM / Synechocystis sp. PCC 6803 / Syn6803 / Transcription initiation / CTP-bound RPitc / Transcription / Cyanobacteria / TRANSCRIPTION-DNA-RNA complex | |||||||||
Function / homology | Function and homology information sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | You LL / Shen LQ / Zhang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc Authors: You LL / Shen LQ / Zhang Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34398.map.gz | 8.6 MB | EMDB map data format | |
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Header (meta data) | emd-34398-v30.xml emd-34398.xml | 30.4 KB 30.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34398_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_34398.png | 178.6 KB | ||
Masks | emd_34398_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-34398.cif.gz | 9 KB | ||
Others | emd_34398_additional_1.map.gz emd_34398_half_map_1.map.gz emd_34398_half_map_2.map.gz | 65.6 MB 65.6 MB 65.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34398 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34398 | HTTPS FTP |
-Validation report
Summary document | emd_34398_validation.pdf.gz | 843.9 KB | Display | EMDB validaton report |
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Full document | emd_34398_full_validation.pdf.gz | 843.5 KB | Display | |
Data in XML | emd_34398_validation.xml.gz | 17 KB | Display | |
Data in CIF | emd_34398_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34398 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34398 | HTTPS FTP |
-Related structure data
Related structure data | 8gzhMC 8gzgC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34398.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Mask #1
File | emd_34398_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_34398_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34398_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34398_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc
+Supramolecule #1: The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit gamma
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: RNA polymerase sigma factor SigA
+Macromolecule #6: DNA-directed RNA polymerase subunit beta'
+Macromolecule #7: Nontemplate strand DNA
+Macromolecule #8: Template strand DNA
+Macromolecule #9: RNA (5'-R(*CP*CP*GP*A)-3')
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ZINC ION
+Macromolecule #12: CYTIDINE-5'-TRIPHOSPHATE
-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 / Support film - Material: GOLD / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 135 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2297 / 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: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8gzh: |