[English] 日本語
Yorodumi- PDB-7ksq: The Structure of the moss PSI-LHCI reveals the evolution of the L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ksq | ||||||
---|---|---|---|---|---|---|---|
Title | The Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna | ||||||
Components |
| ||||||
Keywords | PHOTOSYNTHESIS / PSI / electron transport / chlorophyll / Antenna / light harvesting / membrane protein | ||||||
Function / homology | Function and homology information photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Physcomitrium patens (plant) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Riddle, R. / Gorski, C. / Toporik, H. / Dobson, Z. / Da, Z. / Williams, D. / Mazor, Y. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Nat Plants / Year: 2022 Title: The structure of the Physcomitrium patens photosystem I reveals a unique Lhca2 paralogue replacing Lhca4. Authors: C Gorski / R Riddle / H Toporik / Z Da / Z Dobson / D Williams / Y Mazor / Abstract: The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary ...The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red-shifted Lhca4 antennae are present in the photosystem I light-harvesting complex of many green-lineage plants but absent in P. patens. The cryo-EM structure of the P. patens photosystem I light-harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in Cyanobacteria and several algal species but lost in vascular plants, and the PsaO subunit responsible for binding light-harvesting complex II. The blue-shifted Lhca2 paralogue and chlorophyll b enrichment relative to flowering plants make the P. patens PSI-LHCI spectroscopically unique among other green-lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent-shaped LHCI common in vascular plants, and contains a unique Lhca2 paralogue that facilitates the moss's adaptation to low-light niches. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ksq.cif.gz | 809.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ksq.ent.gz | 725.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ksq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/7ksq ftp://data.pdbj.org/pub/pdb/validation_reports/ks/7ksq | HTTPS FTP |
---|
-Related structure data
Related structure data | 23023MC 7ku5C 7kuxC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 82313.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q8MFA3, photosystem I |
---|---|
#2: Protein | Mass: 82245.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q8MFA2, photosystem I |
-Chlorophyll a-b binding protein, ... , 4 types, 4 molecules 1234
#3: Protein | Mass: 20761.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9T399 |
---|---|
#4: Protein | Mass: 22124.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1IW94 |
#5: Protein | Mass: 23834.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9TEM8 |
#6: Protein | Mass: 22305.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9RW10 |
-Protein , 9 types, 9 molecules CDEFGHKLO
#7: Protein | Mass: 8649.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXQ2, photosystem I |
---|---|
#8: Protein | Mass: 15789.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9REG3 |
#9: Protein | Mass: 7081.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9SPD7 |
#10: Protein | Mass: 17646.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1IN36 |
#11: Protein | Mass: 9728.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9SJ10 |
#12: Protein | Mass: 9491.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9TCU9 |
#15: Protein | Mass: 8106.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JLW2 |
#16: Protein | Mass: 16692.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9S1E1 |
#18: Protein | Mass: 9778.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JDE1 |
-Photosystem I reaction center subunit ... , 3 types, 3 molecules IJM
#13: Protein/peptide | Mass: 3791.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXR3 |
---|---|
#14: Protein/peptide | Mass: 4597.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXM2 |
#17: Protein/peptide | Mass: 3179.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXK4 |
-Sugars , 2 types, 7 molecules
#26: Sugar | ChemComp-LMT / #27: Sugar | ChemComp-DGD / | |
---|
-Non-polymers , 10 types, 257 molecules
#19: Chemical | ChemComp-CL0 / | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#20: Chemical | ChemComp-CLA / #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-BCR / #24: Chemical | ChemComp-LHG / #25: Chemical | ChemComp-LMG / #28: Chemical | ChemComp-CHL / #29: Chemical | ChemComp-LUT / ( #30: Water | ChemComp-HOH / | |
-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: PSI / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
---|---|
Source (natural) | Organism: Physcomitrium patens (plant) |
Buffer solution | pH: 8 |
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 3.1 / Category: final Euler assignment |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114608 / Symmetry type: POINT |