+Open data
-Basic information
Entry | Database: PDB / ID: 8w9z | ||||||
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Title | The cryo-EM structure of the Nicotiana tabacum PEP-PAP | ||||||
Components |
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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 / thylakoid membrane organization / chloroplast organization / acid-amino acid ligase activity / chloroplast thylakoid ...plastid-encoded plastid RNA polymerase complex / etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid organization / chloroplast nucleoid / thylakoid membrane organization / chloroplast organization / acid-amino acid ligase activity / chloroplast thylakoid / disulfide oxidoreductase activity / thylakoid / protein-lysine N-methyltransferase activity / biosynthetic process / plastid / superoxide dismutase / superoxide dismutase activity / protein-disulfide reductase activity / response to light stimulus / DNA-directed RNA polymerase complex / cell redox homeostasis / chloroplast / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Wu, X.X. / Zhang, Y. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w9z.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8w9z.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8w9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w9z_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8w9z_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8w9z_validation.xml.gz | 178.6 KB | Display | |
Data in CIF | 8w9z_validation.cif.gz | 298.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/8w9z ftp://data.pdbj.org/pub/pdb/validation_reports/w9/8w9z | HTTPS FTP |
-Related structure data
Related structure data | 37386MC 8wa0C 8wa1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules AaBCc
#1: Protein | Mass: 38663.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P06269 #2: Protein | | Mass: 120698.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P06271 #3: Protein | | Mass: 79367.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A140G1Q3 #4: Protein | | Mass: 157057.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P38550 |
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-Protein , 8 types, 9 molecules DEGKLMmNP
#5: Protein | Mass: 101413.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) | ||||
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#6: Protein | Mass: 96666.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZSI0 | ||||
#8: Protein | Mass: 30420.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CKK0 | ||||
#13: Protein | Mass: 38014.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZQT7 | ||||
#14: Protein | Mass: 34825.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CIZ9 | ||||
#15: Protein | Mass: 20142.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YEW3 #16: Protein | | Mass: 85288.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D4H1 #18: Protein | | Mass: 17054.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YU01 |
-Protein PLASTID TRANSCRIPTIONALLY ACTIVE ... , 4 types, 4 molecules FHJO
#7: Protein | Mass: 80402.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YXM6 |
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#9: Protein | Mass: 61281.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YPU3 |
#12: Protein | Mass: 58183.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D7C7 |
#17: Protein | Mass: 19254.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XP85 |
-Fructokinase-like ... , 2 types, 2 molecules Ii
#10: Protein | Mass: 55770.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CE74 |
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#11: Protein | Mass: 72534.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BFK7 |
-Non-polymers , 3 types, 4 molecules
#19: Chemical | ChemComp-ZN / |
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#20: Chemical | ChemComp-MG / |
#21: Chemical |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Nicotiana tabacum PEP-PAP / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: Nicotiana tabacum (common tobacco) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 410910 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 163.35 Å2 | ||||||||||||||||||||||||
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