+
Open data
-
Basic information
Entry | Database: PDB / ID: 8wa0 | ||||||
---|---|---|---|---|---|---|---|
Title | The cryo-EM structure of the Nicotiana tabacum PEP-PAP-TEC1 | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / PEP / PAP | ||||||
Function / homology | ![]() 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
![]() | Wu, X.X. / Zhang, Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 194 KB | Display | |
Data in CIF | ![]() | 325.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37387MC ![]() 8w9zC ![]() 8wa1C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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) ![]() ![]() #2: Protein | | Mass: 120698.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 79367.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 157057.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-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) ![]() ![]() | ||||
---|---|---|---|---|---|
#6: Protein | Mass: 96666.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#8: Protein | Mass: 30420.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#13: Protein | Mass: 38014.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#14: Protein | Mass: 34825.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#15: Protein | Mass: 20142.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | | Mass: 85288.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | | Mass: 17054.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
---|---|
#9: Protein | Mass: 61281.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 58183.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 17619.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
---|---|
#11: Protein | Mass: 72534.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA chain / RNA chain , 2 types, 2 molecules RS
#19: DNA chain | Mass: 14633.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#20: RNA chain | Mass: 6446.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FE.gif)
#21: Chemical | ChemComp-ZN / |
---|---|
#22: Chemical | ChemComp-MG / |
#23: Chemical |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Nicotiana tabacum PEP-PAP-TEC1 / Type: COMPLEX / Entity ID: #1-#20 / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: ![]() ![]() |
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42911 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 152.78 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|