The structure of photosystem I from a high-light-tolerant cyanobacteria
- School of Molecular Sciences, Arizona State University, United States
- BiodesignCenter for Applied Structural Discovery, Arizona State University, United States
- Department of Chemistry, Purdue University, United States
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, United States
Figures
Figure 1
Isolation of a high-light-tolerant cyanobacteria.
(A) Cross-sectional negative stained image of C. aponinum fixed in acrylic medium. (B) Phylogenetic analysis based on C. aponinum 16 S rRNA. Evolutionary analyses were conducted in MEGA7. (C) Serial …
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Figure 1—source data 1
Source data for Figure 1.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig1-data1-v2.zip
Figure 2 with 1 supplement
Isolation and characterization of trimeric PSI.
(A) Ten percent to 30% sucrose gradient of solubilized C. aponinum membranes following an anion exchange chromatography. (B) SDS–PAGE of the main sucrose gradient band (Trimer) compared to PSI …
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Figure 2—source data 1
Source data for Figure 2.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig2-data1-v2.zip
Figure 2—figure supplement 1
Photosystem I protein sequence alignment comparison between C.
aponinum and Synechocystis.
Figure 3 with 6 supplements
The structure of trimeric PSI from C. aponinum.
(A) C. aponinum trimeric PSI (B) chlorophyll B40 shifts its position due to the insertion seen in the PsaB subunit in C. aponinum (green) compared to Synechocystis (black). (C) The PsaL subunits of C…
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Figure 3—source data 1
Source data for Figure 3.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig3-data1-v2.zip
Figure 3—figure supplement 1
Cryo-EM data processing.
(A) Workflow of CryoEM image processing. (B) A representation micrograph together with the power spectrum and CTF fit. (C) Representative 2D class averages generated from unsupervised 2D …
Figure 3—figure supplement 2
Model resolution and map examples.
(A) The final 3D map colored according to the local resolution estimates obtained from ResMap,. (B) Plots of the fourier shell correlation (FSC) against resolution. (C) Representative map sections …
Figure 3—figure supplement 3
The local environment of Chl1240.
(A) Structural comparison surrounding the CHL1240 coordination across PSI from different species. (B) Protein sequence of the loop region. The mutation made into Synechocystis is outlined in black.
Figure 3—figure supplement 4
Comparison of the PsaL subunits from C.
aponinum (green), Synechocystis (black), and Pisum Sativum (purple) including the PsaH subunit (pink) in Pisum sativum.
Figure 3—figure supplement 5
Ca2+ coordinating residue in prokaryotes.
A bar graph representing the frequency of different amino acids in cyanobacteria at the position corresponding to PsaL-D73 in Synechocystis. Negatively charged residues such as aspartate (D) or …
Figure 3—figure supplement 6
A bar graph representing the frequency of different amino acids in eukaryotes, and their side chain properties, at the position which would coordinate the Ca2+ ion observed in early cyanobacteria structures.
This is made from 459 sequences.
Figure 4 with 1 supplement
Spectroscopic analysis of Red_c.
(A) Ten percent to 30% sucrose gradient of solubilized membranes from WT Synechocystis, Red_c, and Red_d after purification by anion exchange. (B) SDS–PAGE of the main sucrose gradient bands in …
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Figure 4—source data 1
Source data for Figure 4.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig4-data1-v2.zip
Figure 4—figure supplement 1
Solubilized membranes of WT Synechocystis and Red_d before anion exchange, displaying the increased relative ratio of PSI monomers to trimers in vivo in Red_d.
Figure 5
Calculated transition dipole vectors for chlorophylls B18, B19, and B40.
Viewed from above (A) or beside (B) the plane of pigment B19. The structures are aligned relative to the main ring atoms of chlorophylls B18 and B19. Red atoms/dipoles refer to WT Synechocystis, …
Figure 6 with 4 supplements
Local protein environment of predicted LWC.
(A) The location of chlorophyll B7 and A32 within each monomer, C. aponinum (green), and WT Synechocystis (gray, LWC in red). (B) The surrounding environment for chlorophyll B7 and A32 with C. …
Figure 6—figure supplement 1
Overlay of C.
aponinum, Synechocystis, and Pisum Sativum showing the local protein environment around chlorophylls A31/A32/B7.
Figure 6—figure supplement 2
PsaI20 amino acid frequency among 320 bacteria sequences (left) and 581 eukaryote sequences (right).
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Figure 6—figure supplement 2—source data 1
Source data for Figure 6—figure supplement 2.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig6-figsupp2-data1-v2.zip
Figure 6—figure supplement 3
PsaL65 amino acid frequency among 680 bacteria sequences (left) and 459 eukaryote sequences (right).
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Figure 6—figure supplement 3—source data 1
Source data for Figure 6—figure supplement 3.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig6-figsupp3-data1-v2.zip
Figure 6—figure supplement 4
PsaA446 amino acid frequency among 774 bacteria sequences (left) and 356 eukaryote sequences (right).
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Figure 6—figure supplement 4—source data 1
Source data for Figure 6—figure supplement 4.
- https://cdn.elifesciences.org/articles/67518/elife-67518-fig6-figsupp4-data1-v2.zip
Tables
Table 1
Cryo-EM data collection, refinement, and validation statistics.
| PSI complex(EMD-21320, PDB-6VPV) | |
|---|---|
| Data collection and processing | |
| Calibrated pixel size (Å)Detector, physical pixel size (µm) | 1.05K2 summit, 5 |
| Voltage (kV) | 300 |
| Total electron dose (e–/Å2) | 61 |
| Defocus range (μm) | –1.5 to – 3.0 |
| Super pixel size (Å) | 0.525 |
| Symmetry imposed | C3 |
| Initial particle images (no.) | 256,410 |
| Final particle images (no.) | 73,984 |
| Map resolution (Å) | 2.7 |
| FSC threshold | 0.143 |
| Map resolution range (Å) | 2.1–4.1 |
| Refinement | |
| Initial model used (PDB code) | 5OY0 |
| Model resolution (Å) | 2.7 |
| FSC threshold | 0.143 |
| Model resolution range (Å) | 2.1–4.1 |
| Map sharpening B factor (Å2) | –72.48 |
| Model composition | |
| Nonhydrogen atoms | 71,814 |
| Protein residues | 6,743 |
| Ligands | 384 |
| B factors (Å2) | |
| Protein | 50.00/137.33/86.61 |
| Ligand | 27.10/131.48/54.64 |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.005 |
| Bond angles (°) | 0.894 |
| Validation | |
| MolProbity score | 1.82 |
| Clashscore | 10.36 |
| Poor rotamers (%) | 0.0 |
| Ramachandran plot | |
| Favored (%) | 95.89 |
| Allowed (%) | 4.11 |
| Disallowed (%) | 0 |
Table 2
Site energies and calculated coupling values amongst chlorophylls B18, B19, and B40 for WT Synechocystis and C. aponinum structures.
| B18 | B19 | B40 | |
|---|---|---|---|
| B18 | 14,600 | –71 | –20 |
| B19 | –59 | 14,950 | –106 |
| B40 | –10 | –70 | 14,950 |
Additional files
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Supplementary file 1
(1a) Individual chains and ligand resolvability according to Q-scores.
Scores were calculated using the MapQ plugin in UCSFChimera. (1b). Primer list used for mutant construction.
- https://cdn.elifesciences.org/articles/67518/elife-67518-supp1-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/67518/elife-67518-transrepform1-v2.docx
