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Yorodumi- EMDB-44438: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent tra... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44438 | |||||||||
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Title | Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA | |||||||||
Map data | composite map | |||||||||
Sample |
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Keywords | RNA polymerase / pre-termination complex / FttA / archaea / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information exonuclease activity / transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...exonuclease activity / transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / Hydrolases; Acting on ester bonds / protein dimerization activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermococcus kodakarensis (archaea) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | You L / Ebright RH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structural basis of archaeal FttA-dependent transcription termination Authors: You L / Ebright RH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44438.map.gz | 116.3 MB | EMDB map data format | |
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Header (meta data) | emd-44438-v30.xml emd-44438.xml | 29.9 KB 29.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44438_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_44438.png | 152 KB | ||
Filedesc metadata | emd-44438.cif.gz | 9.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44438 | HTTPS FTP |
-Related structure data
Related structure data | 9bctMC 9bcuC C: citing same article (ref.) 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_44438.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | composite map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : FttA-dependent transcription termination complex
+Supramolecule #1: FttA-dependent transcription termination complex
+Macromolecule #1: DNA-directed RNA polymerase subunit A'
+Macromolecule #2: DNA-directed RNA polymerase subunit B
+Macromolecule #3: DNA-directed RNA polymerase subunit A"
+Macromolecule #4: DNA-directed RNA polymerase subunit D
+Macromolecule #5: DNA-directed RNA polymerase subunit E
+Macromolecule #6: DNA-directed RNA polymerase subunit F
+Macromolecule #7: DNA-directed RNA polymerase subunit H
+Macromolecule #8: DNA-directed RNA polymerase subunit K
+Macromolecule #9: DNA-directed RNA polymerase subunit L
+Macromolecule #10: DNA-directed RNA polymerase subunit N
+Macromolecule #11: DNA-directed RNA polymerase subunit P
+Macromolecule #12: Transcription elongation factor Spt5
+Macromolecule #13: Transcription elongation factor Spt4
+Macromolecule #14: Transcription termination factor FttA
+Macromolecule #15: non-template strand DNA
+Macromolecule #16: template strand DNA
+Macromolecule #17: RNA
+Macromolecule #18: MAGNESIUM ION
+Macromolecule #19: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / 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) / 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 / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-9bct: |