[English] 日本語
Yorodumi- EMDB-3694: In situ subtomogram average of Rubisco within the Chlamydomonas p... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3694 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | In situ subtomogram average of Rubisco within the Chlamydomonas pyrenoid | |||||||||
Map data | In situ subtomogram average of Rubisco holoenzymes within the pyrenoid of Chlamydomonas reinhardtii. Filtered to 16%u212B. | |||||||||
Sample |
| |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 16.5 Å | |||||||||
Authors | Cuellar LK / Schaffer M / Strauss M / Martinez-Sanchez A / Plitzko JM / Foerster F / Engel BD | |||||||||
Citation | Journal: Cell / Year: 2017 Title: The Eukaryotic CO-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization. Authors: Elizabeth S Freeman Rosenzweig / Bin Xu / Luis Kuhn Cuellar / Antonio Martinez-Sanchez / Miroslava Schaffer / Mike Strauss / Heather N Cartwright / Pierre Ronceray / Jürgen M Plitzko / ...Authors: Elizabeth S Freeman Rosenzweig / Bin Xu / Luis Kuhn Cuellar / Antonio Martinez-Sanchez / Miroslava Schaffer / Mike Strauss / Heather N Cartwright / Pierre Ronceray / Jürgen M Plitzko / Friedrich Förster / Ned S Wingreen / Benjamin D Engel / Luke C M Mackinder / Martin C Jonikas / Abstract: Approximately 30%-40% of global CO fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is ...Approximately 30%-40% of global CO fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is densely packed with the CO-fixing enzyme Rubisco and is thought to be a crystalline or amorphous solid. Here, we show that the pyrenoid matrix of the unicellular alga Chlamydomonas reinhardtii is not crystalline but behaves as a liquid that dissolves and condenses during cell division. Furthermore, we show that new pyrenoids are formed both by fission and de novo assembly. Our modeling predicts the existence of a "magic number" effect associated with special, highly stable heterocomplexes that influences phase separation in liquid-like organelles. This view of the pyrenoid matrix as a phase-separated compartment provides a paradigm for understanding its structure, biogenesis, and regulation. More broadly, our findings expand our understanding of the principles that govern the architecture and inheritance of liquid-like organelles. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3694.map.gz | 638.3 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3694-v30.xml emd-3694.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3694_fsc_1.xml emd_3694_fsc_2.xml | 2.1 KB 2.4 KB | Display Display | FSC data file |
Images | emd_3694.png | 66.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3694 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3694 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3694.map.gz / Format: CCP4 / Size: 686.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | In situ subtomogram average of Rubisco holoenzymes within the pyrenoid of Chlamydomonas reinhardtii. Filtered to 16%u212B. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : In situ Rubisco holoenzyme
Entire | Name: In situ Rubisco holoenzyme |
---|---|
Components |
|
-Supramolecule #1: In situ Rubisco holoenzyme
Supramolecule | Name: In situ Rubisco holoenzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: In situ subtomogram average generated from Rubisco holoenzymes imaged within the native Chlamydomonas pyrenoid. Cells were thinned by focused ion beam milling. |
---|---|
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: mat3-4 |
Molecular weight | Theoretical: 540 KDa |
-Macromolecule #1: Rubisco holoenzyme
Macromolecule | Name: Rubisco holoenzyme / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
---|---|
Sequence | String: MVPQTETKAG AGFKAGVKDY RLTYYTPDYV VRDTDILAAF RMTPQPGVPP EECGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEPV PGEDNQYIAY VAYPIDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYVKTFVG PPHGIQVERD KLNKYGRGLL ...String: MVPQTETKAG AGFKAGVKDY RLTYYTPDYV VRDTDILAAF RMTPQPGVPP EECGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEPV PGEDNQYIAY VAYPIDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYVKTFVG PPHGIQVERD KLNKYGRGLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT KDDENVNSQP FMRWRDRFLF VAEAIYKAQA ETGEVKGHYL NATAGTCEEM MKRAVCAKEL GVPIIMHDYL TGGFTANTSL AIYCRDNGLL LHIHRAMHAV IDRQRNHGIH FRVLAKALRM SGGDHLHSGT VVGKLEGERE VTLGFVDLMR DDYVEKDRSR GIYFTQDWCS MPGVMPVASG GIHVWHMPAL VEIFGDDACL QFGGGTLGHP WGNAPGAAAN RVALEACTQA RNEGRDLARE GGDVIRSACK WSPELAAACE VWKEIKFEFD TIDKL |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV Details: Blotted for 10 seconds with 10 blot force before plunging.. |
Details | Rubisco holoenzymes within the native Chlamydomonas pyrenoid. Whole cells were plunge-frozen onto EM grids and then thinned with a focused ion beam instrument. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 6.457 µm / Calibrated defocus min: 5.077 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 42000 |
Specialist optics | Energy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 1.5 e/Å2 Details: Images were collected in movie mode at 17 frames per second |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|