[English] 日本語
Yorodumi
- PDB-5h2h: A three dimensional movie of structural changes in bacteriorhodop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h2h
TitleA three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 40 ns after photoexcitation
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / bacteriorhodopsin / XFEL / time-resolved serial femtosecond crystallography / SACLA
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / 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
TETRADECANE / DECANE / nonane / HEPTANE / 2,3-DI-PHYTANYL-GLYCEROL / PENTADECANE / N-OCTANE / RETINAL / TRIDECANE / UNDECANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoyant, A. / Nango, E. / Nakane, T. / Tanaka, T. / Arima, T. / Neutze, R. / Iwata, S.
CitationJournal: Science / Year: 2016
Title: A three-dimensional movie of structural changes in bacteriorhodopsin
Authors: Nango, E. / Royant, A. / Kubo, M. / Nakane, T. / Wickstrand, C. / Kimura, T. / Tanaka, T. / Tono, K. / Song, C. / Tanaka, R. / Arima, T. / Yamashita, A. / Kobayashi, J. / Hosaka, T. / ...Authors: Nango, E. / Royant, A. / Kubo, M. / Nakane, T. / Wickstrand, C. / Kimura, T. / Tanaka, T. / Tono, K. / Song, C. / Tanaka, R. / Arima, T. / Yamashita, A. / Kobayashi, J. / Hosaka, T. / Mizohata, E. / Nogly, P. / Sugahara, M. / Nam, D. / Nomura, T. / Shimamura, T. / Im, D. / Fujiwara, T. / Yamanaka, Y. / Jeon, B. / Nishizawa, T. / Oda, K. / Fukuda, M. / Andersson, R. / Bath, P. / Dods, R. / Davidsson, J. / Matsuoka, S. / Kawatake, S. / Murata, M. / Nureki, O. / Owada, S. / Kameshima, T. / Hatsui, T. / Joti, Y. / Schertler, G. / Yabashi, M. / Bondar, A.N. / Standfuss, J. / Neutze, R. / Iwata, S.
History
DepositionOct 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Jan 31, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,89217
Polymers26,8141
Non-polymers4,07816
Water30617
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,67651
Polymers80,4433
Non-polymers12,23348
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area25220 Å2
ΔGint-117 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 62.500, 112.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP residues 14-261 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 (Halophile) / Strain: NRC-1 / References: UniProt: P02945

-
Non-polymers , 11 types, 33 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H88O3
#4: Chemical ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#7: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#8: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32
#9: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24
#10: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#11: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.4 / Details: 0.1M Na/K phosphate pH5.4, 30% PEG 2000

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.63 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.63 Å / Relative weight: 1
ReflectionResolution: 2.1→38.92 Å / Num. obs: 14513 / % possible obs: 100 % / Redundancy: 264 % / CC1/2: 0.988 / Net I/σ(I): 8.87

-
Processing

Software
NameVersionClassification
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHENIX1.10_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6V

5b6v


Resolution: 2.1→21.912 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.174 719 4.97 %
Rwork0.1571 --
obs0.158 14473 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→21.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 242 17 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032123
X-RAY DIFFRACTIONf_angle_d0.8472830
X-RAY DIFFRACTIONf_dihedral_angle_d17.2981229
X-RAY DIFFRACTIONf_chiral_restr0.037315
X-RAY DIFFRACTIONf_plane_restr0.004306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.26210.25081440.21832730X-RAY DIFFRACTION100
2.2621-2.48950.16391310.16032749X-RAY DIFFRACTION100
2.4895-2.84910.1681420.14542771X-RAY DIFFRACTION100
2.8491-3.5870.16951430.15242729X-RAY DIFFRACTION100
3.587-21.91280.17131590.15552775X-RAY DIFFRACTION100

+
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