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Yorodumi- PDB-7pl9: Cryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pl9 | ||||||
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Title | Cryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophin) complex | ||||||
Components | Rhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / Single particle Cryo-EM / rhodopsin | ||||||
Function / homology | RETINAL Function and homology information | ||||||
Biological species | Phaeocystis (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å | ||||||
Authors | Matzov, D. / Kaczmarczyk, I. / Shalev-Benami, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels. Authors: Andrey Rozenberg / Igor Kaczmarczyk / Donna Matzov / Johannes Vierock / Takashi Nagata / Masahiro Sugiura / Kota Katayama / Yuma Kawasaki / Masae Konno / Yujiro Nagasaka / Mako Aoyama / ...Authors: Andrey Rozenberg / Igor Kaczmarczyk / Donna Matzov / Johannes Vierock / Takashi Nagata / Masahiro Sugiura / Kota Katayama / Yuma Kawasaki / Masae Konno / Yujiro Nagasaka / Mako Aoyama / Ishita Das / Efrat Pahima / Jonathan Church / Suliman Adam / Veniamin A Borin / Ariel Chazan / Sandra Augustin / Jonas Wietek / Julien Dine / Yoav Peleg / Akira Kawanabe / Yuichiro Fujiwara / Ofer Yizhar / Mordechai Sheves / Igor Schapiro / Yuji Furutani / Hideki Kandori / Keiichi Inoue / Peter Hegemann / Oded Béjà / Moran Shalev-Benami / Abstract: Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a ...Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pl9.cif.gz | 838.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pl9.ent.gz | 679.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pl9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7pl9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7pl9_validation.xml.gz | 117.8 KB | Display | |
Data in CIF | 7pl9_validation.cif.gz | 162.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/7pl9 ftp://data.pdbj.org/pub/pdb/validation_reports/pl/7pl9 | HTTPS FTP |
-Related structure data
Related structure data | 13485MC 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
#1: Protein | Mass: 134010.250 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaeocystis (eukaryote) / Production host: Spodoptera frugiperda (fall armyworm) #2: Chemical | ChemComp-RET / 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: Rhodopsin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.67 MDa / Experimental value: NO |
Source (natural) | Organism: Phaeocystis antarctica (eukaryote) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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 |
Image recording | Electron dose: 0.86 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27749 / Symmetry type: POINT |