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- PDB-7pl9: Cryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophi... -

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Basic information

Entry
Database: PDB / ID: 7pl9
TitleCryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophin) complex
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / Single particle Cryo-EM / rhodopsin
Function / homologyRETINAL
Function and homology information
Biological speciesPhaeocystis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsMatzov, D. / Kaczmarczyk, I. / Shalev-Benami, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionAug 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
C: Rhodopsin
D: Rhodopsin
E: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)671,47310
Polymers670,0515
Non-polymers1,4225
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39200 Å2
ΔGint-284 kcal/mol
Surface area219320 Å2

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Components

#1: Protein
Rhodopsin


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 / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rhodopsin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.67 MDa / Experimental value: NO
Source (natural)Organism: Phaeocystis antarctica (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 0.86 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27749 / Symmetry type: POINT

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