[English] 日本語
Yorodumi
- EMDB-13485: Cryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13485
TitleCryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophin) complex
Map dataSharpened cryoEM map
Sample
  • Complex: Rhodopsin
    • Protein or peptide: Rhodopsin
  • Ligand: RETINAL
Biological speciesPhaeocystis antarctica (eukaryote) / Phaeocystis (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsMatzov D / Kaczmarczyk I / Shalev-Benami M
Funding support1 items
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, 2021-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13485.png

Downloads & links

-
Map

FileDownload / File: emd_13485.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryoEM map
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.02919818 - 0.067163505
Average (Standard dev.)-0.0001643096 (±0.001908686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened cryoEM map

Fileemd_13485_additional_1.map
AnnotationUnsharpened cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_13485_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_13485_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Rhodopsin

EntireName: Rhodopsin
Components
  • Complex: Rhodopsin
    • Protein or peptide: Rhodopsin
  • Ligand: RETINAL

-
Supramolecule #1: Rhodopsin

SupramoleculeName: Rhodopsin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Phaeocystis antarctica (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 670 KDa

-
Macromolecule #1: Rhodopsin

MacromoleculeName: Rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Phaeocystis (eukaryote)
Molecular weightTheoretical: 134.01025 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASSTAAPPA AVPAIETAAP PSPEPRDSVS VNEGGDASSA QAGAAVGSTI IVGAPELEKE YSDLNFAQVA RDEGRRCLLM CVAFAIAIA HLYIYPALFG VRIVDQAEVP AEERTYFHHG WTAMLVIFFI EGVTVFLKVC STRKTRWLEK AVLQKLDGNI G VLIGEYIV ...String:
MASSTAAPPA AVPAIETAAP PSPEPRDSVS VNEGGDASSA QAGAAVGSTI IVGAPELEKE YSDLNFAQVA RDEGRRCLLM CVAFAIAIA HLYIYPALFG VRIVDQAEVP AEERTYFHHG WTAMLVIFFI EGVTVFLKVC STRKTRWLEK AVLQKLDGNI G VLIGEYIV VAATYIIMGA NLIPVFEEPR SGRRVYAVRY MEWTIDACGL VYLDCRILFG MPFSKFRMLL VYSVLYMLFG LW AALASTW MWYAIFLSAS WFFFGLVCYY YWTFHRQNPS PLQQFGRAPI KQAILVFVIV WWVLYGVLFM LCFQAPDVVP QWL EQLLWT GMDVVMKLSH TVVLMAWRET QWEIDAVVDR QKVEAGRAIA QLDHQRAIHE RDLVRLRSRV YYGEHIKSEE EIKS EEVIS RSLRARKSRQ GQDGTEPSSA LSGASSTKEP PALEENSGSA APSWTAVLAK GKATSSPFAR VNKIFMREAG LCLVL CLAF VVALLHLPVY SEWFGVEVLD AEAVPHDELG FFHHGWTTML VVFLIESITV LLKVWSTWHD PRLAENVAQQ LSGNLG VLI AEYLVVGATY VILGYNLMPV FVVHRPGVAS RRVYAVRYME WAVDATGLIW LDCHCLFSRN FNEFRMAIVW TVAYMLF GL WSALASTWAW YWAFLLASWA AFLIVCLILV RFLRQDPYPH QPFGKTSVKP CILAFIIGWW VLYGILFMVC FQAPDAVP Q WLEQFLWTGM DVVMKLSHTV VLMAWRTTEW NVCELHGRNQ AEKSKKSLLN EGSHARQEKQ QLEAIMLEGG GVEAAGRVG SVSFAPSSSR RRKESDSTNW TATPGLRVDL SSMVRLEGQL AQGLVTDVHR KGMMRSEDLA ELKRLEESGF LQAQQHRNWE SQTREMTFL AHGINHIAYD PRSWMKTLTA VRGRAPTSFL LWVVLIESSI VLALSKFFGE SFDLGVSSGI HSLFGVLVSF L VVFRTQAA FKKWWSGRSA VSSLVQMSRT FAQQVCAYVK DEAYVNRMVR YSIATVVATR CHLRNTRIDP AMLLGVLKEE EI EELNRQK NLPFYTAWVI RSTLAEAVAE GACLPLHMAI ENAIKAIEQS IADAERLLTP MPFTYVVHVR TFLFIYLMGL PFI LVEDLG WLMLVAVSFL GYLMIGLENT AVQLENPFGT DCNHHPLDLY CLEVSQDLLH LLDLRASAKA Q

-
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 / Retinal

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 0.86 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27749

+
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