[English] 日本語
Yorodumi
- PDB-1at9: STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELEC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1at9
TitleSTRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY
ComponentsBACTERIORHODOPSIN
KeywordsPHOTORECEPTOR / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / TWO-DIMENSIONAL CRYSTAL
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / 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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.8 Å
AuthorsKimura, Y. / Vassylyev, D.G. / Miyazawa, A. / Kidera, A. / Matsushima, M. / Mitsuoka, K. / Murata, K. / Hirai, T. / Fujiyoshi, Y.
Citation
Journal: Nature / Year: 1997
Title: Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.
Authors: Y Kimura / D G Vassylyev / A Miyazawa / A Kidera / M Matsushima / K Mitsuoka / K Murata / T Hirai / Y Fujiyoshi /
Abstract: Bacteriorhodopsin is a transmembrane protein that uses light energy, absorbed by its chromophore retinal, to pump protons from the cytoplasm of bacteria such as Halobacterium salinarium into the ...Bacteriorhodopsin is a transmembrane protein that uses light energy, absorbed by its chromophore retinal, to pump protons from the cytoplasm of bacteria such as Halobacterium salinarium into the extracellular space. It is made up of seven alpha-helices, and in the bacterium forms natural, two-dimensional crystals called purple membranes. We have analysed these crystals by electron cryo-microscopy to obtain images of bacteriorhodopsin at 3.0 A resolution. The structure covers nearly all 248 amino acids, including loops outside the membrane, and reveals the distribution of charged residues on both sides of the membrane surface. In addition, analysis of the electron-potential map produced by this method allows the determination of the charge status of these residues. On the extracellular side, four glutamate residues surround the entrance to the proton channel, whereas on the cytoplasmic side, four aspartic acids occur in a plane at the boundary of the hydrophobic-hydrophilic interface. The negative charges produced by these aspartate residues is encircled by areas of positive charge that may facilitate accumulation and lateral movement of protons on this surface.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Electron-Crystallographic Refinement of the Structure of Bacteriorhodopsin
Authors: Grigorieff, N. / Ceska, T.A. / Downing, K.H. / Baldwin, J.M. / Henderson, R.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Model for the Structure of Bacteriorhodopsin Based on High-Resolution Electron Cryo-Microscopy
Authors: Henderson, R. / Baldwin, J.M. / Ceska, T.A. / Zemlin, F. / Beckmann, E. / Downing, K.H.
History
DepositionAug 20, 1997-
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Movie
  • Biological unit as author_and_software_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0822
Polymers26,7971
Non-polymers2841
Water0
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2456
Polymers80,3923
Non-polymers8533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6740 Å2
ΔGint-54 kcal/mol
Surface area28890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.450, 62.450, 100.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein BACTERIORHODOPSIN /


Mass: 26797.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: JW5 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
Compound detailsTHE SURFACE STRUCTURE IS NEW AND UNIQUE. ALPHA CARBONS' POSITIONS ARE SIMILAR TO 2BRD EXCEPT FOR ...THE SURFACE STRUCTURE IS NEW AND UNIQUE. ALPHA CARBONS' POSITIONS ARE SIMILAR TO 2BRD EXCEPT FOR THOSE NEAR THE MEMBRANE SURFACES. SOME OF THE SIDE CHAINS DIFFER CONSIDERABLY FROM 2BRD EVEN IN THE MIDDLE PART OF HELICES.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Bacteriorhodopsin / Type: COMPLEX / Source: NATURAL
Buffer solutionpH: 5.5 / Details: 0.4 M citric acid Na2HPO4, 3% trehalose
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: specially ordered surface-polished to minimize wrinkles induced by cryo-fixation
Grid material: MOLYBDENUM
EM embeddingDetails: 3% trehalose / Material: trehalose
VitrificationInstrument: REICHERT-JUNG PLUNGER / Cryogen name: ETHANE / Details: delay of 10 seconds before rapid freezing
CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 71 %
Crystal grow
*PLUS
Method: other / Details: Oesterhelt, D., (1974) Methods Enzymol., 31, 667.

-
Data collection

EM imaging

Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Temperature (max): 4.2 K / Temperature (min): 4.2 K / Specimen-ID: 1

IDAccelerating voltage (kV)ModelMode
1400JEOL 4000DIFFRACTION
2300JEOL 3000SFFBRIGHT FIELDBright-field microscopy
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector model
111510GENERIC GATAN (2k x 2k)
22210KODAK SO-163 FILM
DetectorDate: Apr 1, 1992
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 9531 / % possible obs: 89 % / Num. measured all: 185305 / Rmerge(I) obs: 0.156

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
EM softwareName: CCP4 programs / Category: crystallography merging
3D reconstructionResolution: 2.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL
RefinementHighest resolution: 3 Å
Details: POSITIONAL REFINEMENT. ORIGINAL MODEL WAS PUBLISHED WITHOUT ANY REFINEMENT. A MODEL WAS PLACED TO FIT TO THE EXPERIMENTALLY OBTAINED MAP AND WAS CHECKED WITH RAMACHANDRAN PLOT BY USING ...Details: POSITIONAL REFINEMENT. ORIGINAL MODEL WAS PUBLISHED WITHOUT ANY REFINEMENT. A MODEL WAS PLACED TO FIT TO THE EXPERIMENTALLY OBTAINED MAP AND WAS CHECKED WITH RAMACHANDRAN PLOT BY USING PROGRAM:PROCHECK. IT SHOWED A CONFIGURATION WITH RESIDUES 80.9% IN MOST FAVORABLE REGIONS, 15.5% IN ADDITIONAL ALLOWED REGIONS, 3.6% IN GENEROUSLY ALLOWED REGIONS AND 0% IN DISALLOWED REGIONS. SPECIAL POSITION/STRUCTURE DETERMINATION THE STRUCTURE WAS DETERMINED FROM TWO DIMENSIONAL CRYSTALS AND THEREFORE THE POSITION IN THE DIRECTION ALONG C AXIS IS ARBITRARY. IN ORDER TO HAVE POSITION OF THE CURRENT MODEL COMPARABLE TO 1BRD AND 2BRD IN PDB, THE AUTHORS FITTED THE MODEL TO 2BRD BY USING LSQ_EXP AND LSQ_MOL FUNCTIONS IN 4D_ONO PROGRAM AUTHORED BY ALWYN JONES. THE MATCHED POSITIONS ARE CA IN THE FOLLOWING ZONES: 10-25, 43-60, 82-98, 113-126, 135-145, 175-190, 204-222.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 20 0 1798
Refinement
*PLUS
Rfactor obs: 0.24 / Rfactor Rfree: 0.37
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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