[English] 日本語
Yorodumi
- PDB-9jou: Cryo-EM structure of the zeaxanthin-bound light-driven proton pum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jou
TitleCryo-EM structure of the zeaxanthin-bound light-driven proton pumping rhodopsin, NM-R1
ComponentsProteorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin / zeaxanthin
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
DODECANE / Zeaxanthin / HEXADECANE / RETINAL / Proteorhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsHosaka, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Intracellular carotenoids enhance the pump activation of microbial rhodopsin in two ways: The light-harvesting antenna and the photocycle acceleration
Authors: Fujiwara, T. / Hosaka, T. / Hasegawa-Takano, M. / Nishimura, Y. / Tominaga, K. / Mori, K. / Nishino, S. / Kawasaki, Y. / Takahashi, Y. / Uchikubo-Kamo, T. / Hanada, K. / Takaichi, S. / ...Authors: Fujiwara, T. / Hosaka, T. / Hasegawa-Takano, M. / Nishimura, Y. / Tominaga, K. / Mori, K. / Nishino, S. / Kawasaki, Y. / Takahashi, Y. / Uchikubo-Kamo, T. / Hanada, K. / Takaichi, S. / Inoue, K. / Shirouzu, M. / Yoshizawa, S.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)156,66240
Polymers147,4075
Non-polymers9,25435
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Proteorhodopsin / NM-R1


Mass: 29481.465 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: NMS_0162 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZ92

-
Non-polymers , 5 types, 86 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K3I / Zeaxanthin / zeaxanthin


Mass: 568.871 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: NM-R1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1814697 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementResolution: 2.46→2.46 Å / Cor.coef. Fo:Fc: 0.815 / SU B: 10.168 / SU ML: 0.221 / ESU R: 0.214
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.42286 --
obs0.42286 210458 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 121.649 Å2
Refinement stepCycle: 1 / Total: 9913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01210167
ELECTRON MICROSCOPYr_bond_other_d00.0169964
ELECTRON MICROSCOPYr_angle_refined_deg1.5311.77713707
ELECTRON MICROSCOPYr_angle_other_deg0.5681.6922770
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.53551145
ELECTRON MICROSCOPYr_dihedral_angle_2_deg19.8615.882170
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.98101425
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0890.21410
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0211730
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022620
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it11.67211.2824595
ELECTRON MICROSCOPYr_mcbond_other11.67211.2824595
ELECTRON MICROSCOPYr_mcangle_it16.44320.1985735
ELECTRON MICROSCOPYr_mcangle_other16.44220.2035736
ELECTRON MICROSCOPYr_scbond_it11.30113.1885572
ELECTRON MICROSCOPYr_scbond_other11.313.195573
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other17.99224.0147973
ELECTRON MICROSCOPYr_long_range_B_refined25.696112.112677
ELECTRON MICROSCOPYr_long_range_B_other25.687112.1112675
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.607 15552 -
obs--100 %

+
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