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Yorodumi- PDB-7wlm: The Cryo-EM structure of siphonaxanthin chlorophyll a/b type ligh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wlm | ||||||
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Title | The Cryo-EM structure of siphonaxanthin chlorophyll a/b type light-harvesting complex II | ||||||
Components | siphonaxanthin chlorophyll a/b binding light-harvesting complex II | ||||||
Keywords | PHOTOSYNTHESIS / light-harvesting complex II / siphonaxanthin / Chlorophyll b replacement / blue-green utilization | ||||||
Function / homology | Siphonaxanthin / Siphonein / CHLOROPHYLL B / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-NEX Function and homology information | ||||||
Biological species | Codium fragile (dead man's fingers) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Seki, S. / Nakaniwa, T. / Castro-Hartmann, P. / Sader, K. / Kawamoto, A. / Tanaka, H. / Qian, P. / Kurisu, G. / Fujii, R. | ||||||
Funding support | 1items
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Citation | Journal: BBA Adv / Year: 2022 Title: Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 Å. Authors: Soichiro Seki / Tetsuko Nakaniwa / Pablo Castro-Hartmann / Kasim Sader / Akihiro Kawamoto / Hideaki Tanaka / Pu Qian / Genji Kurisu / Ritsuko Fujii / Abstract: Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, , exhibits the unique characteristic of ...Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, , exhibits the unique characteristic of absorbing blue-green light from the sun during photochemical reactions while being underwater owing to the presence of pigment-altered LHCII called siphonaxanthin-chlorophyll binding protein (SCP). In this study, we determined the structure of SCP at a resolution of 2.78 Å using cryogenic electron microscopy. SCP has a trimeric structure, wherein each monomer containing two lutein and two chlorophyll molecules in the plant-type LHCII are replaced by siphonaxanthin and its ester and two chlorophyll molecules, respectively. Siphonaxanthin occupies the binding site in SCP having a polarity in the trimeric inner core, and exhibits a distorted conjugated chain comprising a carbonyl group hydrogen bonded to a cysteine residue of apoprotein. These features suggest that the siphonaxanthin molecule is responsible for the characteristic green absorption of SCP. The replaced chlorophyll molecules extend the region of the stromal side chlorophyll cluster, spanning two adjacent monomers. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wlm.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wlm.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/7wlm ftp://data.pdbj.org/pub/pdb/validation_reports/wl/7wlm | HTTPS FTP |
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-Related structure data
Related structure data | 32588MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 24190.102 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Codium fragile (dead man's fingers) / Strain: KU-0654 |
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-Non-polymers , 7 types, 105 molecules
#2: Chemical | ChemComp-CHL / #3: Chemical | ChemComp-CLA / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: siphonaxanthin chlorophyll a/b-type light-harvesting complex II Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.119 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Codium fragile (dead man's fingers) | |||||||||||||||
Buffer solution | pH: 8.2 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER | |||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50.75 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 8935 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2336076 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250633 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1RWT Pdb chain-ID: B / Accession code: 1RWT / Pdb chain residue range: 14-231 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
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