[English] 日本語
Yorodumi
- EMDB-11955: Cryo-EM structure of the green-light absorbing proteorhodopsin -

+
Open data


ID or keywords:

Loading...

-
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
KeywordsLight-driven proton pump / microbial rhodopsin / retinal / PROTON TRANSPORT
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane
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
Green-light absorbing proteorhodopsin
Similarity search - Component
Biological speciesuncultured Gammaproteobacteria bacterium (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHirschi S / Kalbermatter 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

-
Structure visualization

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

emd_11955.png

Downloads & links

-
Map

FileDownload / File: emd_11955.map.gz / Format: CCP4 / Size: 1.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.29 Å/pix.
x 82 pix.
= 105.78 Å		1.29 Å/pix.
x 80 pix.
= 103.2 Å		1.29 Å/pix.
x 48 pix.
= 61.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-2.6761472 - 4.288378
Average (Standard dev.)0.000000000009905 (±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

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

UniProtKB: Green-light absorbing proteorhodopsin

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
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

-
Image processing

Startup modelType of model: NONE
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more