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- EMDB-11955: Cryo-EM structure of the green-light absorbing proteorhodopsin -

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Basic information

Entry
Database: EMDB / ID: EMD-11955
TitleCryo-EM structure of the green-light absorbing proteorhodopsin
Map data
Sample
  • Complex: Pentamer of the green-light absorbing proteorhodopsin
    • Protein or peptide: Proteorhodopsin
  • Ligand: RETINAL
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / : / photoreceptor activity / phototransduction / membrane => GO:0016020
Similarity search - Function
Proteorhodopsin / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Biological speciesuncultured Gammaproteobacteria bacterium (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHirschi S / Kalbermatter D / Fotiadis D
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin.
Authors: Stephan Hirschi / David Kalbermatter / Zöhre Ucurum / Thomas Lemmin / Dimitrios Fotiadis /
Abstract: The green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important ...The green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important residues of the proton translocation pathway and the oligomerization interface. Superposition with the structure of a close GPR homolog and molecular dynamics simulations reveal conformational variations, which regulate the solvent access to the intra- and extracellular half channels harbouring the primary proton donor E109 and the proposed proton release group E143. We provide a mechanism for the structural rearrangements allowing hydration of the intracellular half channel, which are triggered by changing the protonation state of E109. Functional characterization of selected mutants demonstrates the importance of the molecular organization around E109 and E143 for GPR activity. Furthermore, we present evidence that helices involved in the stabilization of the protomer interfaces serve as scaffolds for facilitating the motion of the other helices. Combined with the more constrained dynamics of the pentamer compared to the monomer, these observations illustrate the previously demonstrated functional significance of GPR oligomerization. Overall, this work provides molecular insights into the structure, dynamics and function of the proteorhodopsin family that will benefit the large scientific community employing GPR as a model protein.
History
DepositionNov 18, 2020-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b03
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b03
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11955.png

Downloads & links

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Map

FileDownload / File: emd_11955.map.gz / Format: CCP4 / Size: 1.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.29 Å
Density
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-2.6761472 - 4.288378
Average (Standard dev.)9.905457e-12 (±0.44219473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin688869
Dimensions804882
Spacing828048
CellA: 105.78 Å / B: 103.2 Å / C: 61.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z828048
origin x/y/z0.0000.0000.000
length x/y/z105.780103.20061.920
α/β/γ90.00090.00090.000
start NX/NY/NZ696888
NX/NY/NZ828048
MAP C/R/S321
start NC/NR/NS886869
NC/NR/NS488082
D min/max/mean-2.6764.2880.000

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Supplemental data

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Sample components

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Entire : Pentamer of the green-light absorbing proteorhodopsin

EntireName: Pentamer of the green-light absorbing proteorhodopsin
Components
  • Complex: Pentamer of the green-light absorbing proteorhodopsin
    • Protein or peptide: Proteorhodopsin
  • Ligand: RETINAL

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Supramolecule #1: Pentamer of the green-light absorbing proteorhodopsin

SupramoleculeName: Pentamer of the green-light absorbing proteorhodopsin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: uncultured Gammaproteobacteria bacterium (environmental samples)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Proteorhodopsin

MacromoleculeName: Proteorhodopsin / type: protein_or_peptide / ID: 1 / Details: Expressed without signal sequence. / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: uncultured Gammaproteobacteria bacterium (environmental samples)
Molecular weightTheoretical: 25.611842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGGGDLDAS DYTGVSFWLV TAALLASTVF FFVERDRVSA KWKTSLTVSG LVTGIAFWHY MYMRGVWIET GDSPTVFRYI DWLLTVPLL ICEFYLILAA ATNVAGSLFK KLLVGSLVML VFGYMGEAGI MAAWPAFIIG CLAWVYMIYE LWAGEGKSAC N TASPAVQS ...String:
MAGGGDLDAS DYTGVSFWLV TAALLASTVF FFVERDRVSA KWKTSLTVSG LVTGIAFWHY MYMRGVWIET GDSPTVFRYI DWLLTVPLL ICEFYLILAA ATNVAGSLFK KLLVGSLVML VFGYMGEAGI MAAWPAFIIG CLAWVYMIYE LWAGEGKSAC N TASPAVQS AYNTMMYIII FGWAIYPVGY FTGYLMGDGG SALNLNLIYN LADFVNKILF GLIIWNVAVK ESSNA

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 5 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Final map was obtained after applying density modification using Resolve Cryo-EM in Phenix.
Number images used: 717107
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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