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Yorodumi- EMDB-19023: Plastid-encoded RNA polymerase transcription elongation complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19023 | |||||||||||||||
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Title | Plastid-encoded RNA polymerase transcription elongation complex | |||||||||||||||
Map data | Plastid-encoded RNA polymerase transcription elongation complex | |||||||||||||||
Sample |
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Keywords | Transcription / chloroplast / RNA polymerase / photosynthesis / GENE REGULATION | |||||||||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / chloroplast / 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 Similarity search - Function | |||||||||||||||
Biological species | Sinapis alba (white mustard) / DNA molecule (others) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||||||||
Authors | Webster MW / Pramanick I / Vergara-Cruces A | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Cell / Year: 2024 Title: Structure of the plant plastid-encoded RNA polymerase. Authors: Ángel Vergara-Cruces / Ishika Pramanick / David Pearce / Vinod K Vogirala / Matthew J Byrne / Jason K K Low / Michael W Webster / Abstract: Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded ...Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19023.map.gz | 743.3 MB | EMDB map data format | |
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Header (meta data) | emd-19023-v30.xml emd-19023.xml | 38.3 KB 38.3 KB | Display Display | EMDB header |
Images | emd_19023.png | 109.7 KB | ||
Filedesc metadata | emd-19023.cif.gz | 13 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19023 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19023 | HTTPS FTP |
-Validation report
Summary document | emd_19023_validation.pdf.gz | 641 KB | Display | EMDB validaton report |
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Full document | emd_19023_full_validation.pdf.gz | 640.6 KB | Display | |
Data in XML | emd_19023_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_19023_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19023 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19023 | HTTPS FTP |
-Related structure data
Related structure data | 8rasMC 8rdjMC 8r5oC 8r6sC 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_19023.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Plastid-encoded RNA polymerase transcription elongation complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.5 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Plastid-encoded RNA polymerase transcription elongation complex
+Supramolecule #1: Plastid-encoded RNA polymerase transcription elongation complex
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit beta''
+Macromolecule #5: PAP1
+Macromolecule #6: PAP2
+Macromolecule #7: PAP3
+Macromolecule #8: PAP4
+Macromolecule #9: PAP5
+Macromolecule #10: PAP6
+Macromolecule #11: PAP7
+Macromolecule #12: PAP8
+Macromolecule #13: PAP9
+Macromolecule #14: PAP10
+Macromolecule #15: PAP11
+Macromolecule #16: PAP12
+Macromolecule #17: FLN2
+Macromolecule #18: PTAC18
+Macromolecule #19: DNA (81-MER)
+Macromolecule #20: DNA (81-MER)
+Macromolecule #21: RNA (40-MER)
+Macromolecule #22: MAGNESIUM ION
+Macromolecule #23: ZINC ION
+Macromolecule #24: FE (III) ION
+Macromolecule #25: S-ADENOSYL-L-HOMOCYSTEINE
+Macromolecule #26: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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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: 40.48 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 417374 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |