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Yorodumi- EMDB-1079: Electron crystallography reveals the structure of metarhodopsin I. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1079 | |||||||||
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Title | Electron crystallography reveals the structure of metarhodopsin I. | |||||||||
Map data | Density map of a rhodopsin photostationary state, highly enriched in metarhodopsin I | |||||||||
Sample |
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Function / homology | G protein-coupled opsin signaling pathway => GO:0016056 / Rhodopsin Function and homology information | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Ruprecht JJ / Mielke T / Vogel R / Villa C / Schertler GFX | |||||||||
Citation | Journal: EMBO J / Year: 2004 Title: Electron crystallography reveals the structure of metarhodopsin I. Authors: Jonathan J Ruprecht / Thorsten Mielke / Reiner Vogel / Claudio Villa / Gebhard F X Schertler / Abstract: Rhodopsin is the prototypical G protein-coupled receptor, responsible for detection of dim light in vision. Upon absorption of a photon, rhodopsin undergoes structural changes, characterised by ...Rhodopsin is the prototypical G protein-coupled receptor, responsible for detection of dim light in vision. Upon absorption of a photon, rhodopsin undergoes structural changes, characterised by distinct photointermediates. Currently, only the ground-state structure has been described. We have determined a density map of a photostationary state highly enriched in metarhodopsin I, to a resolution of 5.5 A in the membrane plane, by electron crystallography. The map shows density for helix 8, the cytoplasmic loops, the extracellular plug, all tryptophan residues, an ordered cholesterol molecule and the beta-ionone ring. Comparison of this map with X-ray structures of the ground state reveals that metarhodopsin I formation does not involve large rigid-body movements of helices, but there is a rearrangement close to the bend of helix 6, at the level of the retinal chromophore. There is no gradual build-up of the large conformational change known to accompany metarhodopsin II formation. The protein remains in a conformation similar to that of the ground state until late in the photobleaching process. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1079.map.gz | 14.5 MB | EMDB map data format | |
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Header (meta data) | emd-1079-v30.xml emd-1079.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | 1079.gif | 73.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1079 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1079 | HTTPS FTP |
-Validation report
Summary document | emd_1079_validation.pdf.gz | 235.4 KB | Display | EMDB validaton report |
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Full document | emd_1079_full_validation.pdf.gz | 234.5 KB | Display | |
Data in XML | emd_1079_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1079 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1079 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1079.map.gz / Format: CCP4 / Size: 18.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density map of a rhodopsin photostationary state, highly enriched in metarhodopsin I | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bovine Metarhodopsin I
Entire | Name: Bovine Metarhodopsin I |
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Components |
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-Supramolecule #1000: Bovine Metarhodopsin I
Supramolecule | Name: Bovine Metarhodopsin I / type: sample / ID: 1000 Details: Illuminated to form a photostationary state highly enriched in metarhodopsin I Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Experimental: 39 KDa / Theoretical: 39 KDa |
-Macromolecule #1: Rhodopsin
Macromolecule | Name: Rhodopsin / type: protein_or_peptide / ID: 1 / Name.synonym: Rh / Details: Illuminated to form photostationary state / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine / Tissue: Retina / Cell: Retinal rod cell / Organelle: Membrane / Location in cell: Disk membrane |
Molecular weight | Experimental: 39 KDa / Theoretical: 39 KDa |
Sequence | GO: G protein-coupled opsin signaling pathway => GO:0016056 / InterPro: Rhodopsin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 2D array |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7 Details: 20mM HEPES pH 7, 100 mM NaCl, 10 mM MgCl2, 3 mM NaN3, 4 mM DTT, 4 mM mercaptoethanol, 2.5 % (v/v) isopropanol |
Grid | Details: 300 mesh molybdenum grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 77 K / Instrument: GATAN CRYOPLUNGE 3 Details: Vitrification instrument: Gatan cryoplunge. Vitrification carried out in temperature and humidity-controlled chamber Timed resolved state: Vitrified after illumination of specimen Method: Blot for 20 sec before plunging |
Details | 11 day dialysis at 18 deg C |
Crystal formation | Details: 11 day dialysis at 18 deg C |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 77 K / Max: 77 K / Average: 77 K |
Alignment procedure | Legacy - Astigmatism: corrected at 230,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 87 / Average electron dose: 15 e/Å2 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 59000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 1.41 µm / Nominal defocus min: 0.27 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Side entry liquid-nitrogen cooled Gatan holder Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 60 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: OTHER / Software - Name: MRC |
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Crystal parameters | Unit cell - A: 58.8 Å / Unit cell - B: 83.7 Å / Unit cell - C: 200.0 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Plane group: P 2 21 21 |
CTF correction | Details: Each image |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: B |
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Software | Name: O |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |