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- PDB-7wfe: Right PSI in the cyclic electron transfer supercomplex NDH-PSI fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wfe | ||||||||||||||||||
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Title | Right PSI in the cyclic electron transfer supercomplex NDH-PSI from Arabidopsis | ||||||||||||||||||
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![]() | ELECTRON TRANSPORT / Cylic electron trasport / supercomplex / Arabidopsis / plant | ||||||||||||||||||
Function / homology | ![]() photosystem I antenna complex / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / pigment binding / chloroplast membrane / response to high light intensity / chloroplast thylakoid ...photosystem I antenna complex / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / pigment binding / chloroplast membrane / response to high light intensity / chloroplast thylakoid / plastoglobule / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / protein homodimerization activity / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å | ||||||||||||||||||
![]() | Pan, X.W. / Li, M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. Authors: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li / ![]() ![]() Abstract: Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane- ...Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 790.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 32463MC ![]() 7wfdC ![]() 7wffC ![]() 7wfgC ![]() 7wg5C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules BABB
#1: Protein | Mass: 83315.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 82555.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules BCB1
#3: Protein | Mass: 9049.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#13: Protein | Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Photosystem I reaction center subunit ... , 9 types, 9 molecules BDBEBFBGBHBIBJBKBL
#4: Protein | Mass: 22336.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 24203.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 17103.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 15291.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein/peptide | Mass: 4137.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein/peptide | Mass: 5011.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 13219.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 23070.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Photosystem I chlorophyll a/b-binding protein ... , 3 types, 3 molecules B2B3B5
#14: Protein | Mass: 27782.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#15: Protein | Mass: 29206.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 27830.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 2 types, 4 molecules ![](data/chem/img/LMU.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#22: Sugar | #23: Sugar | ChemComp-DGD / | |
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-Non-polymers , 10 types, 201 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/LMG.gif)
#17: Chemical | ChemComp-CLA / #18: Chemical | #19: Chemical | ChemComp-LHG / #20: Chemical | ChemComp-BCR / #21: Chemical | #24: Chemical | ChemComp-SQD / | #25: Chemical | ChemComp-CHL / #26: Chemical | ChemComp-LUT / ( #27: Chemical | ChemComp-XAT / ( #28: Chemical | ChemComp-LMG / | |
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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 |
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Sample preparation
Component | Name: PSI complex in the NDH-PSI supercomplex of Arabidopsis Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.8 |
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: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136022 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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