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Open data
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Basic information
Entry | Database: PDB / ID: 8r5o | |||||||||||||||
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Title | Plastid-encoded RNA polymerase | |||||||||||||||
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![]() | GENE REGULATION / Transcription / chloroplast / RNA polymerase / photosynthesis | |||||||||||||||
Function / homology | ![]() 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 | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||||||||
![]() | Webster, M.W. / Pramanick, I. / Vergara-Cruces, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 155.1 KB | Display | |
Data in CIF | ![]() | 246 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18935MC ![]() 8r6sC ![]() 8rasC ![]() 8rdjC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 37945.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | | Mass: 121209.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 78761.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A6C0M5W0, DNA-directed RNA polymerase #4: Protein | | Mass: 156388.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 14 types, 15 molecules FGHIJKLMNOPQRST
#5: Protein | Mass: 103467.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
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#6: Protein | Mass: 96112.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#7: Protein | Mass: 79815.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#8: Protein | Mass: 30273.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#9: Protein | Mass: 60884.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#10: Protein | Mass: 52435.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#11: Protein | Mass: 55675.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#12: Protein | Mass: 38039.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#13: Protein | Mass: 34008.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#14: Protein | Mass: 20954.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | | Mass: 85121.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | | Mass: 18835.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | | Mass: 68527.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | | Mass: 16429.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 259 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#19: Chemical | ChemComp-ZN / | ||||
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#20: Chemical | #21: Chemical | ChemComp-SAH / | #22: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: Plastid-encoded RNA polymerase / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3400 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 613537 / Symmetry type: POINT |