+
Open data
-
Basic information
Entry | Database: PDB / ID: 7y8a | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of cryptophyte photosystem I | ||||||
![]() |
| ||||||
![]() | PHOTOSYNTHESIS / Cryptophyte / Photosystem I / evolution | ||||||
Function / homology | ![]() thylakoid membrane / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å | ||||||
![]() | Zhao, L.S. / Zhang, Y.Z. / Liu, L.N. / Li, K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis and evolution of the photosystem I-light-harvesting supercomplex of cryptophyte algae. Authors: Long-Sheng Zhao / Peng Wang / Kang Li / Quan-Bao Zhang / Fei-Yu He / Chun-Yang Li / Hai-Nan Su / Xiu-Lan Chen / Lu-Ning Liu / Yu-Zhong Zhang / ![]() ![]() Abstract: Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) ...Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) as light-harvesting complexes (LHCs). Here, we report the structure of the photosynthetic PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea at 2.7-Å resolution obtained by crygenic electron microscopy. Cryptophyte PSI-ACPI represents a unique PSI-LHCI intermediate in the evolution from red algal to diatom PSI-LHCI. The PSI-ACPI supercomplex is composed of a monomeric PSI core containing 14 subunits, 12 of which originated in red algae, 1 diatom PsaR homolog, and an additional peptide. The PSI core is surrounded by 14 ACPI subunits that form 2 antenna layers: an inner layer with 11 ACPIs surrounding the PSI core and an outer layer containing 3 ACPIs. A pigment-binding subunit that is not present in any other previously characterized PSI-LHCI complexes, ACPI-S, mediates the association and energy transfer between the outer and inner ACPIs. The extensive pigment network of PSI-ACPI ensures efficient light harvesting, energy transfer, and dissipation. Overall, the PSI-LHCI structure identified in this study provides a framework for delineating the mechanisms of energy transfer in cryptophyte PSI-LHCI and for understanding the evolution of photosynthesis in the red lineage, which occurred via secondary endosymbiosis. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 16.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 17.5 MB | Display | |
Data in XML | ![]() | 229.9 KB | Display | |
Data in CIF | ![]() | 285.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33683MC ![]() 7y7bC 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
-Protein , 16 types, 16 molecules 123456789CORXZab
#1: Protein | Mass: 23479.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Protein | Mass: 23400.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 24966.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 23548.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 24055.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 22688.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 24550.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 23700.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 23223.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 8743.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 16253.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: Protein | Mass: 13867.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#23: Protein | Mass: 13975.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Authors do not know how the coordinates align with the sequence and the residue numbering is arbitrary. Source: (natural) ![]() |
#24: Protein | Mass: 25645.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 22270.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 23755.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#10: Protein | Mass: 83493.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#11: Protein | Mass: 82219.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJKLM
#13: Protein | Mass: 15590.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#14: Protein | Mass: 7352.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 20393.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein/peptide | Mass: 3975.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein/peptide | Mass: 4862.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#18: Protein | Mass: 8836.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#19: Protein | Mass: 16490.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#20: Protein/peptide | Mass: 3247.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 2 types, 5 molecules ![](data/chem/img/LMU.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#36: Sugar | #39: Sugar | |
---|
-Non-polymers , 11 types, 352 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/II0.gif)
![](data/chem/img/II3.gif)
![](data/chem/img/IHT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/8CT.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/II0.gif)
![](data/chem/img/II3.gif)
![](data/chem/img/IHT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/8CT.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PQN.gif)
#27: Chemical | ChemComp-CLA / #28: Chemical | ChemComp-KC2 / #29: Chemical | ChemComp-II0 / ( #30: Chemical | #31: Chemical | ChemComp-IHT / ( #32: Chemical | ChemComp-LMG / #33: Chemical | ChemComp-LHG / #34: Chemical | #35: Chemical | ChemComp-8CT / ( #37: Chemical | #38: Chemical | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: photosystem I of cryptophyte / Type: COMPLEX / Entity ID: #1-#26 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 6.5 |
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: 1800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118810 / Symmetry type: POINT |