[English] 日本語
Yorodumi- PDB-8to2: Bottom cylinder of high-resolution phycobilisome quenched by OCP ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8to2 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement) | |||||||||||||||
Components |
| |||||||||||||||
Keywords | PHOTOSYNTHESIS / Complex / light harvesting / pigment | |||||||||||||||
Function / homology | Function and homology information light absorption / Lyases / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity / photosynthesis / lyase activity Similarity search - Function | |||||||||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å | |||||||||||||||
Authors | Sauer, P.V. / Sutter, M. / Cupellini, L. | |||||||||||||||
Funding support | European Union, United States, Czech Republic, 4items
| |||||||||||||||
Citation | Journal: Sci Adv / Year: 2024 Title: Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / ...Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / Eva Nogales / Tomáš Polívka / Benedetta Mennucci / Cheryl A Kerfeld / Abstract: Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) ...Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8to2.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8to2.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 8to2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8to2_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8to2_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 8to2_validation.xml.gz | 136.2 KB | Display | |
Data in CIF | 8to2_validation.cif.gz | 199 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/8to2 ftp://data.pdbj.org/pub/pdb/validation_reports/to/8to2 | HTTPS FTP |
-Related structure data
Related structure data | 41434MC 8to5C 8tpjC 8troC 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
-Protein , 3 types, 3 molecules ABp
#1: Protein | Mass: 100412.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55544 |
---|---|
#2: Protein | Mass: 34684.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74102 |
#9: Protein | Mass: 12927.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: A0A6P1VGS4 |
-Phycobilisome ... , 2 types, 3 molecules CcP
#3: Protein | Mass: 7817.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q02925 #6: Protein | | Mass: 28938.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73093 |
---|
-Allophycocyanin ... , 4 types, 23 molecules DFHJLNfhjlEGIKMOegikmdo
#4: Protein | Mass: 17429.807 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q01951 #5: Protein | Mass: 17231.604 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q01952 #7: Protein | | Mass: 17940.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72870 #8: Protein | | Mass: 18911.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74551 |
---|
-Non-polymers , 2 types, 25 molecules
#10: Chemical | ChemComp-CYC / #11: Chemical | ChemComp-45D / | |
---|
-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: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Details: Manual blotting |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Image processing | Details: Streptavidin lattice was subtracted after movie alignment | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153576 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.17 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|