[English] 日本語
Yorodumi
- PDB-7vgu: Time-resolved serial femtosecond crystallography structure of lig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vgu
TitleTime-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / SACLA serial femtosecond crystallography CELL-FREE SYNTHESIS Bacterial type rhodopsin chloride ion pump rhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / BROMIDE ION / DECANE / HEXANE / RETINAL / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHosaka, T. / Nango, E. / Nakane, T. / Luo, F. / Kimura-Someya, T. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.
Authors: Hosaka, T. / Nomura, T. / Kubo, M. / Nakane, T. / Fangjia, L. / Sekine, S.I. / Ito, T. / Murayama, K. / Ihara, K. / Ehara, H. / Kashiwagi, K. / Katsura, K. / Akasaka, R. / Hisano, T. / ...Authors: Hosaka, T. / Nomura, T. / Kubo, M. / Nakane, T. / Fangjia, L. / Sekine, S.I. / Ito, T. / Murayama, K. / Ihara, K. / Ehara, H. / Kashiwagi, K. / Katsura, K. / Akasaka, R. / Hisano, T. / Tanaka, T. / Tanaka, R. / Arima, T. / Yamashita, A. / Sugahara, M. / Naitow, H. / Matsuura, Y. / Yoshizawa, S. / Tono, K. / Owada, S. / Nureki, O. / Kimura-Someya, T. / Iwata, S. / Nango, E. / Shirouzu, M.
History
DepositionSep 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,00712
Polymers30,7111
Non-polymers1,29611
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint13 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.300, 51.100, 78.400
Angle α, β, γ (deg.)90.000, 131.500, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Chloride pumping rhodopsin


Mass: 30710.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3

-
Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 38% PEG400, 300 mM K phosphate, and 100 mM HEPES (pH7.0)

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7714 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7714 Å / Relative weight: 1
ReflectionResolution: 2.1→42.8 Å / Num. obs: 18261 / % possible obs: 100 % / Redundancy: 363 % / CC1/2: 0.993 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 929 / CC1/2: 0.918
Serial crystallography sample deliveryMethod: injection

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2N

5b2n


Resolution: 2.1→29.36 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 899 4.94 %
Rwork0.1821 17305 -
obs0.1835 18204 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.38 Å2 / Biso mean: 32.8699 Å2 / Biso min: 14.98 Å2
Refinement stepCycle: final / Resolution: 2.1→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 97 55 2228
Biso mean--46.18 41.65 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.230.25111400.20862866300699
2.23-2.40.20231630.176728282991100
2.4-2.650.2061610.172728593020100
2.65-3.030.20931410.175229003041100
3.03-3.810.19031430.172128893032100
3.81-29.360.22151510.190829633114100

+
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