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Yorodumi- EMDB-11029: CryoEM structure of the interaction between Rubisco Activase smal... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11029 | |||||||||
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Title | CryoEM structure of the interaction between Rubisco Activase small-subunit-like (SSUL) domain with Rubisco from Nostoc sp. (strain PCC7120) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | beta barrel / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Wang H / Bracher A | |||||||||
Citation | Journal: Cell / Year: 2020 Title: Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes. Authors: Mirkko Flecken / Huping Wang / Leonhard Popilka / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl / Abstract: Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone ...Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization. | |||||||||
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_11029.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-11029-v30.xml emd-11029.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11029_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_11029.png | 72.6 KB | ||
Filedesc metadata | emd-11029.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11029 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11029 | HTTPS FTP |
-Validation report
Summary document | emd_11029_validation.pdf.gz | 343.4 KB | Display | EMDB validaton report |
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Full document | emd_11029_full_validation.pdf.gz | 342.9 KB | Display | |
Data in XML | emd_11029_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_11029_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11029 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11029 | HTTPS FTP |
-Related structure data
Related structure data | 6z1gMC 6hasC 6z1dC 6z1eC 6z1fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11029.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.885 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex between Rubisco Activase small-subunit-like domain with R...
Entire | Name: Complex between Rubisco Activase small-subunit-like domain with Rubisco from Nostoc sp. (strain PCC7120) |
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Components |
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-Supramolecule #1: Complex between Rubisco Activase small-subunit-like domain with R...
Supramolecule | Name: Complex between Rubisco Activase small-subunit-like domain with Rubisco from Nostoc sp. (strain PCC7120) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Supramolecule #2: SSUL domain of Rca, part of the (Rca)6 hexamer
Supramolecule | Name: SSUL domain of Rca, part of the (Rca)6 hexamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Supramolecule #3: (RbcL)2(RbcS)2 unit of the (RbcL)8(RbcS)8 Rubisco complex
Supramolecule | Name: (RbcL)2(RbcS)2 unit of the (RbcL)8(RbcS)8 Rubisco complex type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 Details: The (RbcL)8(RbcS)8 Rubisco complex has D4 symmetry. The (RbcL)2(RbcS)2 unit has two-fold roational symmetry. |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Macromolecule #1: Ribulose bisphosphate carboxylase/oxygenase activase
Macromolecule | Name: Ribulose bisphosphate carboxylase/oxygenase activase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) |
Molecular weight | Theoretical: 10.266549 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: HLSLETQEQI RQILSQGHKI TFEHVDARRF RTGSWQSCGT LHIDAESDAI STLEACLVDY DGEYVRMVGI DPKGKRRVVE TIIQRPNGK N UniProtKB: Ribulose bisphosphate carboxylase/oxygenase activase |
-Macromolecule #2: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) |
Molecular weight | Theoretical: 53.112125 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTTV WTDLLTDLDR YKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT SIVGNVFGFK ALRALRLEDI RFPVAYIKTF QGPPHGIQVE R DKLNKYGR ...String: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTTV WTDLLTDLDR YKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT SIVGNVFGFK ALRALRLEDI RFPVAYIKTF QGPPHGIQVE R DKLNKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFTKDDENIN SAPFQRWRDR FLFVADAITK AQAETGEIKG HY LNVTAPT CEEMLKRAEY AKELKQPIIM HDYLTAGFTA NTTLARWCRD NGVLLHIHRA MHAVIDRQKN HGIHFRVLAK ALR LSGGDH IHTGTVVGKL EGERGITMGF VDLLRENYVE QDKSRGIYFT QDWASLPGVM AVASGGIHVW HMPALVEIFG DDSV LQFGG GTLGHPWGNA PGATANRVAL EACVQARNEG RNLAREGNDV IREAAKWSPE LAVACELWKE IKFEFEAMDT V UniProtKB: Ribulose bisphosphate carboxylase large chain |
-Macromolecule #3: Ribulose bisphosphate carboxylase small chain
Macromolecule | Name: Ribulose bisphosphate carboxylase small chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) |
Molecular weight | Theoretical: 12.840725 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MQTLPKERRY ETLSYLPPLT DVQIEKQVQY ILSQGYIPAV EFNEVSEPTE LYWTLWKLPL FGAKTSREVL AEVQSCRSQY PGHYIRVVG FDNIKQCQIL SFIVHKPSRY UniProtKB: Ribulose bisphosphate carboxylase small subunit |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.9 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||
Details | For Preparing the NosRca:Rubisco complex, NosRubisco (1.25 uM) was mixed with NosRca (15 uM). |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 1570 / Average exposure time: 12.0 sec. / Average electron dose: 47.0 e/Å2 / Details: 40 frames per image |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6z1g: |