+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37386 | |||||||||
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Title | The cryo-EM structure of the Nicotiana tabacum PEP-PAP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TRANSCRIPTION / PEP / PAP | |||||||||
Function / homology | Function and homology information plastid-encoded plastid RNA polymerase complex / etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid organization / chloroplast nucleoid / chloroplast organization / acid-amino acid ligase activity / disulfide oxidoreductase activity / biosynthetic process ...plastid-encoded plastid RNA polymerase complex / etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid organization / chloroplast nucleoid / chloroplast organization / acid-amino acid ligase activity / disulfide oxidoreductase activity / biosynthetic process / superoxide dismutase / superoxide dismutase activity / protein-disulfide reductase activity / response to light stimulus / DNA-directed RNA polymerase complex / chloroplast / cell redox homeostasis / methyltransferase activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / kinase activity / regulation of cell shape / methylation / protein dimerization activity / cell division / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Nicotiana tabacum (common tobacco) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Wu XX / Zhang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell / Year: 2024 Title: Cryo-EM structures of the plant plastid-encoded RNA polymerase. Authors: Xiao-Xian Wu / Wen-Hui Mu / Fan Li / Shu-Yi Sun / Chao-Jun Cui / Chanhong Kim / Fei Zhou / Yu Zhang / Abstract: Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast ...Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37386.map.gz | 122.5 MB | EMDB map data format | |
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Header (meta data) | emd-37386-v30.xml emd-37386.xml | 45.9 KB 45.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37386_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_37386.png | 118.9 KB | ||
Filedesc metadata | emd-37386.cif.gz | 12.8 KB | ||
Others | emd_37386_additional_1.map.gz emd_37386_additional_2.map.gz emd_37386_additional_3.map.gz emd_37386_additional_4.map.gz emd_37386_half_map_1.map.gz emd_37386_half_map_2.map.gz | 223.8 MB 224.2 MB 225 MB 225 MB 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37386 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37386 | HTTPS FTP |
-Validation report
Summary document | emd_37386_validation.pdf.gz | 887.6 KB | Display | EMDB validaton report |
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Full document | emd_37386_full_validation.pdf.gz | 887.1 KB | Display | |
Data in XML | emd_37386_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | emd_37386_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37386 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37386 | HTTPS FTP |
-Related structure data
Related structure data | 8w9zMC 8wa0C 8wa1C 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_37386.map.gz / Format: CCP4 / Size: 244.1 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
-Additional map: #4
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-Additional map: #3
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-Additional map: #2
File | emd_37386_additional_3.map | ||||||||||||
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-Additional map: #1
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-Half map: #2
File | emd_37386_half_map_1.map | ||||||||||||
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-Half map: #1
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Density Histograms |
-Sample components
+Entire : Nicotiana tabacum PEP-PAP
+Supramolecule #1: Nicotiana tabacum PEP-PAP
+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 beta''
+Macromolecule #5: PAP1(pTAC3)
+Macromolecule #6: Pentatricopeptide repeat-containing protein At1g74850, chloroplas...
+Macromolecule #7: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10-like
+Macromolecule #8: superoxide dismutase
+Macromolecule #9: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12-like
+Macromolecule #10: Fructokinase-like 1, chloroplastic
+Macromolecule #11: Fructokinase-like 2, chloroplastic
+Macromolecule #12: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14-like isoform X2
+Macromolecule #13: PAP8(pTAC6)
+Macromolecule #14: superoxide dismutase
+Macromolecule #15: Thioredoxin-like protein CITRX1, chloroplastic
+Macromolecule #16: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate l...
+Macromolecule #17: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7-like isoform X1
+Macromolecule #18: PAP13(pTAC18)
+Macromolecule #19: ZINC ION
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: FE (III) ION
-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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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: 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |