+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18049 | ||||||||||||||||||
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Title | Chlorella sorokiniana Rubisco: D4 symmetry imposed | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Rubisco / PLANT PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information L-amino acid transmembrane transporter activity / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding / membrane Similarity search - Function | ||||||||||||||||||
Biological species | Chlorella sorokiniana (plant) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.39 Å | ||||||||||||||||||
Authors | Barrett J / Blaza JN / Mackinder LCM | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: To Be Published Title: A promiscuous mechanism to phase separate eukaryotic carbon fixation Authors: Barrett J / Naduthodi MIS / Mao Y / Degut C / Musial S / Leake MC / Plevin MJ / McCormick AJ / Blaza JN / Mackinder LCM | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18049.map.gz | 12.3 MB | EMDB map data format | |
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Header (meta data) | emd-18049-v30.xml emd-18049.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18049_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_18049.png | 98.6 KB | ||
Masks | emd_18049_msk_1.map | 13.4 MB | Mask map | |
Filedesc metadata | emd-18049.cif.gz | 6.7 KB | ||
Others | emd_18049_half_map_1.map.gz emd_18049_half_map_2.map.gz | 8.1 MB 8.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18049 | HTTPS FTP |
-Validation report
Summary document | emd_18049_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_18049_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_18049_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_18049_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18049 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18049 | HTTPS FTP |
-Related structure data
Related structure data | 8q04MC 8q05C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18049.map.gz / Format: CCP4 / Size: 13.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.148 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18049_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18049_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18049_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rubisco holoenzyme purified from Chlorella sorokiniana UTEX1230
Entire | Name: Rubisco holoenzyme purified from Chlorella sorokiniana UTEX1230 |
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Components |
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-Supramolecule #1: Rubisco holoenzyme purified from Chlorella sorokiniana UTEX1230
Supramolecule | Name: Rubisco holoenzyme purified from Chlorella sorokiniana UTEX1230 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Chlorella sorokiniana (plant) / Strain: UTEX1230 (SAG211-8k) / Organelle: Pyrenoid / Location in cell: Chloroplast |
-Macromolecule #1: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Chlorella sorokiniana (plant) / Strain: UTEX1230 (SAG211-8k) |
Molecular weight | Theoretical: 52.580418 KDa |
Sequence | String: MAPQTETRAG AGFKAGVKDY RLTYYTPDYQ PKDTDILAAF RMTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEP VPGEENQYIA YIAYPLDLFE EGSVTNLFTS IVGNVFGFKA LRALRLEDLR IPPAYVKTFQ GPPHGIQVER D KLNKYGRG ...String: MAPQTETRAG AGFKAGVKDY RLTYYTPDYQ PKDTDILAAF RMTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEP VPGEENQYIA YIAYPLDLFE EGSVTNLFTS IVGNVFGFKA LRALRLEDLR IPPAYVKTFQ GPPHGIQVER D KLNKYGRG LLGCTIKPKL GLSAKNYGRA VYECLRGGLD FTKDDENVNS QPFMRWRDRF LFVAEAIYKS QAETGEIKGH YL NATAATA EEMLKRAECA KDLGVPIIMH DYLTGGFTAN TSLAHYCRDN GLLLHIHRAM HAVIDRQRNH GIHFRVLAKA LRL SGGDHL HSGTVVGKLE GEREVTLGFV DLMRDDYIEK DRSRGIYFTQ DWVSLPGTMP VASGGIHVWH MPALVEIFGD DACL QFGGG TLGHPWGNAP GAAANRVALE ACTQARNEGR DLAREGGDVI RAACKWSPEL AAACEVWKEI KFEFETIDTL UniProtKB: Ribulose bisphosphate carboxylase large chain |
-Macromolecule #2: Ribulose bisphosphate carboxylase small subunit, chloroplastic
Macromolecule | Name: Ribulose bisphosphate carboxylase small subunit, chloroplastic type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlorella sorokiniana (plant) / Strain: UTEX1230 (SAG211-8k) |
Molecular weight | Theoretical: 20.507385 KDa |
Sequence | String: MACTIAAVAP VAVRPVAATP LKQARNTFAA RTVSNATIKK TTAMQVWTPL NNKFFETFSY LPPMTDAEIS RQVDYIVSNG WTPCLEFAG AESAYTSNEN CVRMQNTTCL YYDNRYWTMW KLPMFGCTDG GQVLREVQAC RRAFPDAYIR VVGFDPVRQV Q VSGFLVNR PASVRDYQGP STRSV UniProtKB: Ribulose bisphosphate carboxylase small subunit, chloroplastic |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 1255 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||||||||
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Buffer | pH: 6.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: Pressure was not recorded | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | Chlorella sorokiniana Rubisco at 0.3 mg/mL (0.5 micromolar) was incubated with alpha3-alpha4 at 16 micromolar. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4447 / Average exposure time: 6.52 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Initial rigid body fitting was completed in UCSF Chimrea. Flexible fitting was completed in COOT and the coordinates were real-space refined in Phenix. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 44 |
Output model | PDB-8q04: |