[English] 日本語
Yorodumi
- PDB-5uk6: Structure of Anabaena Sensory Rhodopsin Determined by Solid State... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uk6
TitleStructure of Anabaena Sensory Rhodopsin Determined by Solid State NMR Spectroscopy and DEER
ComponentsBacteriorhodopsin
KeywordsSIGNALING PROTEIN / Anabeana sensory rhodopsin / Trimer / Seven-transmembrane proteins
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodSOLID-STATE NMR
AuthorsMilikisiyants, S. / Wang, S. / Munro, R.A. / Donohue, M. / Ward, M.E. / Brown, L.S. / Smirnova, T.I. / Ladizhansky, V. / Smirnov, A.I.
Funding support United States, Canada, China, 5items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-02ER15354 United States
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-04547 Canada
National Natural Science Foundation of China (NSFC)31470727 China
National Science Foundation (NSF, United States)DBI-1229547 United States
Ministry of Science and Technology (MoST, China)2016YFA0501203 China
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints.
Authors: Milikisiyants, S. / Wang, S. / Munro, R.A. / Donohue, M. / Ward, M.E. / Bolton, D. / Brown, L.S. / Smirnova, T.I. / Ladizhansky, V. / Smirnov, A.I.
History
DepositionJan 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
C: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)82,5373
Polymers82,5373
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -
Representative

-
Components

#1: Protein Bacteriorhodopsin


Mass: 27512.262 Da / Num. of mol.: 3 / Fragment: UNP residues 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr3165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YSC4

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NCA
121isotropic12D PDSD
131isotropic1CONCA
141isotropic1NCACX
151isotropic1NCOCX

-
Sample preparation

DetailsType: liposome
Contents: 2.0 w/w [U-100% 13C; U-100% 15N] UCNASR, DMPC/DMPA
Label: ASR / Solvent system: DMPC/DMPA
SampleConc.: 2.0 w/v / Component: UCNASR / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: NA Not defined / Label: ASR-PL / pH: 7.0 / Pressure: 1 atm / Temperature: 278 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospinrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMR ensembleConformers submitted total number: 10

+
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://pdbjlvh1.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