[English] 日本語
Yorodumi
- PDB-8rss: Crystal structure of marine actinobacteria clade rhodopsin (MAR) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rss
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the O* state
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / Mac / MacR / MAR / proteorhodopsin / PR / xanthorodopsin / XR / xanthorhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / OLEIC ACID / RETINAL / Bacteriorhodopsin
Function and homology information
Biological speciesCandidatus Actinomarina minuta (bacteria)
marine Actinobacteria clade (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBukhdruker, S. / Kovalev, K. / Astashkin, R. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Sci Adv / Year: 2025
Title: Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.
Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / ...Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / Kuklina, D. / Caramello, N. / Rokitskaya, T. / Antonenko, Y. / Rulev, M. / Stoev, C. / Zabelskii, D. / Round, E. / Rogachev, A. / Borshchevskiy, V. / Ghai, R. / Bourenkov, G. / Zeghouf, M. / Cherfils, J. / Engelhard, M. / Chizhov, I. / Rodriguez-Valera, F. / Bamberg, E. / Gordeliy, V.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_keywords.text
Revision 1.2Jul 2, 2025Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,51716
Polymers24,2771
Non-polymers4,24015
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint19 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.608, 40.174, 60.307
Angle α, β, γ (deg.)90.000, 101.220, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

-
Components

#1: Protein Bacteriorhodopsin


Mass: 24277.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: S5DM51
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.4 / Details: 2.6 M Ammonium Phosphate buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.41→40.17 Å / Num. obs: 27492 / % possible obs: 88.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 14.12 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.047 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
4.5-40.172.419.713740.9990.01992.4
1.41-1.551.71.313750.7090.34446.5

-
Processing

Software
NameVersionClassification
XDS20220110data reduction
STARANISO2.3.94data scaling
PHASER2.8.4phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→40.17 Å / SU ML: 0.1103 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 1347 4.9 %
Rwork0.1594 26139 -
obs0.1612 27486 60.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.08 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 137 147 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282116
X-RAY DIFFRACTIONf_angle_d0.57912852
X-RAY DIFFRACTIONf_chiral_restr0.0558301
X-RAY DIFFRACTIONf_plane_restr0.004352
X-RAY DIFFRACTIONf_dihedral_angle_d13.5717812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.460.179120.1934150X-RAY DIFFRACTION3.39
1.47-1.520.2362350.1643639X-RAY DIFFRACTION14.89
1.52-1.590.2432880.18331483X-RAY DIFFRACTION34.45
1.59-1.680.23421230.17022195X-RAY DIFFRACTION50.93
1.68-1.780.22581250.17182566X-RAY DIFFRACTION59.64
1.78-1.920.22431500.16952932X-RAY DIFFRACTION67.54
1.92-2.110.19621710.15763493X-RAY DIFFRACTION80.28
2.11-2.420.18342200.14574241X-RAY DIFFRACTION96.98
2.42-3.050.18692120.1534218X-RAY DIFFRACTION96.56
3.05-40.170.19622210.16424222X-RAY DIFFRACTION94.43

+
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