+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ewk | ||||||
---|---|---|---|---|---|---|---|
Title | Barley photosystem I-LHCI-Lhca6 supercomplex | ||||||
![]() |
| ||||||
![]() | PHOTOSYNTHESIS / Photosystem I / Light-harvesting complex / Lhca6 / cyclic electron transport | ||||||
Function / homology | ![]() photosynthesis, light harvesting in photosystem I / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting in photosystem I / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||
![]() | Wang, W.D. / Shen, L. / Tang, K. / Han, G.Y. / Zhang, X. / Shen, J.R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare. Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang / ![]() ![]() Abstract: The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex ...The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 804.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 680.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 31350MC ![]() 7eu3C ![]() 7ew6C ![]() 7f9oC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 82292.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: S4Z1K7, photosystem I |
---|---|
#2: Protein | Mass: 82562.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: S4Z289, photosystem I |
-Protein , 2 types, 2 molecules C4
#3: Protein | Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
---|---|
#14: Protein | Mass: 21976.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFHIJKL
#4: Protein | Mass: 15801.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
---|---|
#5: Protein | Mass: 7679.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
#6: Protein | Mass: 17488.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
#7: Protein | Mass: 6431.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
#8: Protein/peptide | Mass: 3338.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: S4Z1D9 |
#9: Protein/peptide | Mass: 4747.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: S4Z1E9 |
#10: Protein | Mass: 8502.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
#11: Protein | Mass: 15512.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
-Chlorophyll a-b binding protein ... , 3 types, 3 molecules 136
#12: Protein | Mass: 21278.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
---|---|
#13: Protein | Mass: 24395.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
#15: Protein | Mass: 23904.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
-Sugars , 1 types, 2 molecules ![](data/chem/img/DGD.gif)
#22: Sugar |
---|
-Non-polymers , 10 types, 194 molecules ![](data/chem/img/CL0.gif)
![](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/LMG.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/XAT.gif)
![](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/LMG.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/XAT.gif)
#16: Chemical | ChemComp-CL0 / | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#17: Chemical | ChemComp-CLA / #18: Chemical | #19: Chemical | ChemComp-LHG / #20: Chemical | ChemComp-BCR / #21: Chemical | #23: Chemical | #24: Chemical | ChemComp-LUT / ( #25: Chemical | ChemComp-CHL / #26: 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: PSI-LHCI-Lhca6 supercomplex of Barley / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL |
---|---|
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 / Humidity: 100 % |
-
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: 2500 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT |