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Yorodumi- PDB-8qma: Structure of the plastid-encoded RNA polymerase complex (PEP) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qma | ||||||||||||||||||
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Title | Structure of the plastid-encoded RNA polymerase complex (PEP) from Sinapis alba | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Chloroplasts / Gene Expression / RNA / Polymerase | ||||||||||||||||||
Function / homology | Function and homology information chloroplast / DNA-directed RNA polymerase complex / 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) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | do Prado, P.F.V. / Ahrens, F.M. / Pfannschmidt, T. / Hillen, H.S. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: Mol Cell / Year: 2024 Title: Structure of the multi-subunit chloroplast RNA polymerase. Authors: Paula F V do Prado / Frederik M Ahrens / Monique Liebers / Noah Ditz / Hans-Peter Braun / Thomas Pfannschmidt / Hauke S Hillen / Abstract: Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase ...Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qma.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qma.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/8qma ftp://data.pdbj.org/pub/pdb/validation_reports/qm/8qma | HTTPS FTP |
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-Related structure data
Related structure data | 18496MC 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
-Protein , 13 types, 14 molecules GHKLMNOPRSEFIJ
#1: Protein | Mass: 30404.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) | ||||||||||||||||
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#2: Protein | Mass: 60884.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) | ||||||||||||||||
#3: Protein | Mass: 38039.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) | ||||||||||||||||
#4: Protein | Mass: 34008.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) | ||||||||||||||||
#5: Protein | Mass: 20851.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #6: Protein | | Mass: 85061.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #7: Protein | | Mass: 18835.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #8: Protein | | Mass: 16430.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #9: Protein | | Mass: 52435.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #13: Protein | | Mass: 103467.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #14: Protein | | Mass: 79815.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #15: Protein | | Mass: 68527.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) #16: Protein | | Mass: 55675.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDT
#10: Protein | Mass: 121163.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) References: UniProt: A0A6C0M5W1, DNA-directed RNA polymerase | ||
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#11: Protein | Mass: 156388.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) / References: UniProt: A0A6C0M829 | ||
#12: Protein | Mass: 37885.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) References: UniProt: A0A6C0M610, DNA-directed RNA polymerase #17: Protein | | Mass: 78761.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) References: UniProt: A0A6C0M5W0, DNA-directed RNA polymerase |
-Non-polymers , 3 types, 4 molecules
#18: Chemical | #19: Chemical | ChemComp-ZN / | #20: Chemical | ChemComp-SAM / | |
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-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 |
-Sample preparation
Component | Name: Plastid-encoded DNA-dependent RNA polymerase (PEP) / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Sinapis alba (white mustard) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.7 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123874 / Algorithm: BACK PROJECTION / Symmetry type: POINT |