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- EMDB-1079: Electron crystallography reveals the structure of metarhodopsin I. -

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Basic information

Entry
Database: EMDB / ID: EMD-1079
TitleElectron crystallography reveals the structure of metarhodopsin I.
Map dataDensity map of a rhodopsin photostationary state, highly enriched in metarhodopsin I
Sample
  • Sample: Bovine Metarhodopsin I
  • Protein or peptide: Rhodopsin
Function / homologyG protein-coupled opsin signaling pathway => GO:0016056 / Rhodopsin
Function and homology information
Biological speciesBos taurus (domestic cattle)
Methodelectron crystallography / cryo EM / Resolution: 5.5 Å
AuthorsRuprecht JJ / Mielke T / Vogel R / Villa C / Schertler GFX
CitationJournal: 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
DepositionMay 12, 2004-
Header (metadata) releaseMay 12, 2004-
Map releaseSep 7, 2004-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 51.246035785
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 51.246035785
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1079.gif

Downloads & links

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Map

FileDownload / File: emd_1079.map.gz / Format: CCP4 / Size: 18.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of a rhodopsin photostationary state, highly enriched in metarhodopsin I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.67 Å/pix.
x 119 pix.
= 200. Å		0.49 Å/pix.
x 181 pix.
= 58.8 Å		0.44 Å/pix.
x 231 pix.
= 83.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel size
XYZ
EMDB info.0.490.440531.66667
CCP4 map header0.490.440531.66667
EM Navigator Movie #10.440530.491.6667
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 25.0 / Movie #1: 51.2460358
Minimum - Maximum-131.953247070000003 - 250.0
Average (Standard dev.)-0.29949433 (±28.60485268)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-30-20-59
Dimensions181231119
Spacing190120120
CellA: 58.800003 Å / B: 83.69994 Å / C: 200.0004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.490.440526315789471.6666666666667
M x/y/z120190120
origin x/y/z0.0000.0000.000
length x/y/z58.80083.700200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-20-59
NX/NY/NZ181231119
MAP C/R/S213
start NC/NR/NS-20-30-59
NC/NR/NS231181119
D min/max/mean-131.953250.000-0.299

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Supplemental data

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Sample components

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Entire : Bovine Metarhodopsin I

EntireName: Bovine Metarhodopsin I
Components
  • Sample: Bovine Metarhodopsin I
  • Protein or peptide: Rhodopsin

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Supramolecule #1000: Bovine Metarhodopsin I

SupramoleculeName: 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
Molecular weightExperimental: 39 KDa / Theoretical: 39 KDa

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Macromolecule #1: Rhodopsin

MacromoleculeName: 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
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: Bovine / Tissue: Retina / Cell: Retinal rod cell / Organelle: Membrane / Location in cell: Disk membrane
Molecular weightExperimental: 39 KDa / Theoretical: 39 KDa
SequenceGO: G protein-coupled opsin signaling pathway => GO:0016056 / InterPro: Rhodopsin

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 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
GridDetails: 300 mesh molybdenum grid
VitrificationCryogen 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
Details11 day dialysis at 18 deg C
Crystal formationDetails: 11 day dialysis at 18 deg C

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 77 K / Max: 77 K / Average: 77 K
Alignment procedureLegacy - Astigmatism: corrected at 230,000 times magnification
Image recordingCategory: 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 min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen 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

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: OTHER / Software - Name: MRC
Crystal parametersUnit 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 correctionDetails: Each image

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Atomic model buiding 1

Initial modelPDB ID:

1gzm


Chain - Chain ID: B
SoftwareName: O
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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