[English] 日本語
Yorodumi
- EMDB-3694: In situ subtomogram average of Rubisco within the Chlamydomonas p... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3694
TitleIn situ subtomogram average of Rubisco within the Chlamydomonas pyrenoid
SampleIn situ Rubisco holoenzyme
SourceChlamydomonas reinhardtii / plant
Map dataIn situ subtomogram average of Rubisco holoenzymes within the pyrenoid of Chlamydomonas reinhardtii. Filtered to 16%u212B.
Methodsubtomogram averaging, at 16.5 A resolution
AuthorsCuellar LK / Schaffer M / Strauss M / Martinez-Sanchez A / Plitzko JM / Foerster F / Engel BD
CitationTo be published

To be published Search PubMed
The eukaryotic CO2-concentrating organelle is liquid-like and exhibits dynamic reorganization
Rosenzweig ESF / Xu B / Cuellar LK / Martinez-Sanchez A / Schaffer M / Strauss M / Cartwright HN / Plitzko JM / Foerster F / Wingreen NS / Engel BD / Mackinder LCM / Jonikas MC

DateDeposition: Apr 26, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Apr 26, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_3694.map.gz (map file in CCP4 format, 703 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
56 pix
3.42 A/pix
= 191.52 A
56 pix
3.42 A/pix
= 191.52 A
56 pix
3.42 A/pix
= 191.52 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.42 A
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-5.7059126 - 3.9495337
Average (Standard dev.)3.168763E-9 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions565656
Origin000
Limit555555
Spacing565656
CellA=B=C: 191.52 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z3.423.423.42
M x/y/z565656
origin x/y/z0.0000.0000.000
length x/y/z191.520191.520191.520
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS565656
D min/max/mean-5.7063.9500.000

-
Supplemental data

-
Sample components

-
Entire In situ Rubisco holoenzyme

EntireName: In situ Rubisco holoenzyme
Details: In situ subtomogram average generated from Rubisco holoenzymes imaged within the native Chlamydomonas pyrenoid. Cells were thinned by focused ion beam milling.
Number of components: 2
MassTheoretical: 540 kDa

-
Component #1: protein, In situ Rubisco holoenzyme

ProteinName: In situ Rubisco holoenzyme
Details: In situ subtomogram average generated from Rubisco holoenzymes imaged within the native Chlamydomonas pyrenoid. Cells were thinned by focused ion beam milling.
Recombinant expression: No
MassTheoretical: 540 kDa
SourceSpecies: Chlamydomonas reinhardtii / plant / Strain: mat3-4
Source (natural)Organelle: chloroplast / Location in cell: pyrenoid

-
Component #2: protein, Rubisco holoenzyme

ProteinName: Rubisco holoenzyme / Recombinant expression: No

+
Experimental details

-
Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %
Details: Blotted for 10 seconds with 10 blot force before plunging.

-
Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 5000 nm / Energy filter: Gatan / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -62 - 64 deg.
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionDetails: Images were collected in movie mode at 17 frames per second

-
Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: D4 (2*4 fold dihedral)
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION
CTF correction: Defocus of individual tilts was estimated with IMOD's ctfplotter, and CTF correction was performed with ctfphaseflip
Resolution: 16.5 A / Resolution method: FSC 0.143 CUT-OFF
Details: The 30,000 subvolumes with the highest template matching cross-correlation scores were used for the final reconstruction. Cumulative electron dose was restricted for the final average by only using the central 60 degrees of the tilt-series (-30 to +30). 16.5 A (FSC 0.143 cut-off) gold-standard resolution. 15.5 A (FSC 0.3 cut-off) cross-resolution of the full dataset to the crystal structure.
Euler angles: Angles known from tilt-series acquisition.
FSC plot (resolution assessment)

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more