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Yorodumi- EMDB-13825: Single Particle Cryo-EM structure of photosynthetic A4B4-glyceral... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13825 | |||||||||
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Title | Single Particle Cryo-EM structure of photosynthetic A4B4-glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia. | |||||||||
Map data | A4B4 photosynthetic glyceraldehyde 3-phosphate dehydrogenase octamer. | |||||||||
Sample |
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Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) / spinach (spinach) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 Å | |||||||||
Authors | Marotta R / Fermani S / Sparla F / Trost P / Del Giudice A | |||||||||
Funding support | France, 1 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Unravelling the regulation pathway of photosynthetic AB-GAPDH. Authors: Roberto Marotta / Alessandra Del Giudice / Libero Gurrieri / Silvia Fanti / Paolo Swuec / Luciano Galantini / Giuseppe Falini / Paolo Trost / Simona Fermani / Francesca Sparla / Abstract: Oxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic ...Oxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme in the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant isoform is formed by AB heterotetramers and the least abundant by A homotetramers. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and its activity is strictly regulated. While A-GAPDH is regulated by CP12, AB-GAPDH is autonomously regulated through the C-terminal extension (CTE) of its B subunits. Reversible inhibition of AB-GAPDH occurs via the oxidation of a cysteine pair located in the CTE and the substitution of NADP(H) with NAD(H) in the cofactor-binding site. These combined conditions lead to a change in the oligomerization state and enzyme inhibition. SEC-SAXS and single-particle cryo-EM analysis were applied to reveal the structural basis of this regulatory mechanism. Both approaches revealed that spinach (AB)-GAPDH oligomers with n = 1, 2, 4 and 5 co-exist in a dynamic system. B subunits mediate the contacts between adjacent tetramers in AB and AB oligomers. The CTE of each B subunit penetrates into the active site of a B subunit of the adjacent tetramer, which in turn moves its CTE in the opposite direction, effectively preventing the binding of the substrate 1,3-bisphosphoglycerate in the B subunits. The whole mechanism is made possible, and eventually controlled, by pyridine nucleotides. In fact, NAD(H), by removing NADP(H) from A subunits, allows the entrance of the CTE into the active site of the B subunit, hence stabilizing inhibited oligomers. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13825.map.gz | 8.3 MB | EMDB map data format | |
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Header (meta data) | emd-13825-v30.xml emd-13825.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13825_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_13825.png | 51.2 KB | ||
Others | emd_13825_half_map_1.map.gz emd_13825_half_map_2.map.gz | 46.1 MB 46.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13825 | HTTPS FTP |
-Validation report
Summary document | emd_13825_validation.pdf.gz | 635.6 KB | Display | EMDB validaton report |
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Full document | emd_13825_full_validation.pdf.gz | 635.2 KB | Display | |
Data in XML | emd_13825_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_13825_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13825 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13825 | HTTPS FTP |
-Related structure data
Related structure data | 7q54MC 7q53C 7q55C 7q56C 7q57C 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_13825.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | A4B4 photosynthetic glyceraldehyde 3-phosphate dehydrogenase octamer. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: A4B4 photosynthetic glyceraldehyde 3-phosphate dehydrogenase octamer half map....
File | emd_13825_half_map_1.map | ||||||||||||
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Annotation | A4B4 photosynthetic glyceraldehyde 3-phosphate dehydrogenase octamer half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A4B4 photosynthetic glyceraldehyde 3-phosphate dehydrogenase octamer half map....
File | emd_13825_half_map_2.map | ||||||||||||
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Annotation | A4B4 photosynthetic glyceraldehyde 3-phosphate dehydrogenase octamer half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Photosynthetic A4B4 glyceraldehyde-3-phosphate dehydrogenase hete...
Entire | Name: Photosynthetic A4B4 glyceraldehyde-3-phosphate dehydrogenase hetero-octamer complexed with NAD. |
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Components |
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-Supramolecule #1: Photosynthetic A4B4 glyceraldehyde-3-phosphate dehydrogenase hete...
Supramolecule | Name: Photosynthetic A4B4 glyceraldehyde-3-phosphate dehydrogenase hetero-octamer complexed with NAD. type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Spinacia oleracea (spinach) |
-Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
Macromolecule | Name: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO EC number: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) |
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Source (natural) | Organism: spinach (spinach) |
Molecular weight | Theoretical: 48.183789 KDa |
Sequence | String: MASHAALAPS RIPASTRLAS KASQQYSFLT QCSFKRLDVA DFSGLRSSNS VTFTREASFH DVIAAQLTTK PTGAAPVRGE TVAKLKVAI NGFGRIGRNF LRCWHGRKDS PLDVVVVNDS GGVKSATHLL KYDSILGTFK ADVKIIDNET FSIDGKPIKV V SNRDPLKL ...String: MASHAALAPS RIPASTRLAS KASQQYSFLT QCSFKRLDVA DFSGLRSSNS VTFTREASFH DVIAAQLTTK PTGAAPVRGE TVAKLKVAI NGFGRIGRNF LRCWHGRKDS PLDVVVVNDS GGVKSATHLL KYDSILGTFK ADVKIIDNET FSIDGKPIKV V SNRDPLKL PWAELGIDIV IEGTGVFVDG PGAGKHIQAG AKKVIITAPA KGSDIPTYVV GVNEKDYGHD VANIISNASC TT NCLAPFV KVLDEELGIV KGTMTTTHSY TGDQRLLDAS HRDLRRARAA ALNIVPTSTG AAKAVSLVLP QLKGKLNGIA LRV PTPNVS VVDLVVNIEK VGVTAEDVNN AFRKAAAGPL KGVLDVCDIP LVSVDFRCSD FSSTIDSSLT MVMGGDMVKV VAWY DNEWG YSQRVVDLAD LVANKWPGLE GSVASGDPLE DFCKDNPADE ECKLYE |
-Macromolecule #2: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Macromolecule | Name: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO EC number: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) |
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Source (natural) | Organism: spinach (spinach) |
Molecular weight | Theoretical: 43.159098 KDa |
Sequence | String: MASNMLSIAN PSLRVYNKGF SEFSGLHTSS LPFGRKGSDD LMAFVSFQTN AVGGKRSSQN GVVEAKLKVA INGFGRIGRN FLRCWHGRK DSPLDVVVIN DTGGVKQASH LLKYDSILGT FDADVKTAGD SAISVDGKVI KVVSDRNPVN LPWGDMGIDL V IEGTGVFV ...String: MASNMLSIAN PSLRVYNKGF SEFSGLHTSS LPFGRKGSDD LMAFVSFQTN AVGGKRSSQN GVVEAKLKVA INGFGRIGRN FLRCWHGRK DSPLDVVVIN DTGGVKQASH LLKYDSILGT FDADVKTAGD SAISVDGKVI KVVSDRNPVN LPWGDMGIDL V IEGTGVFV DRDGAGKHLQ AGAKKVLITA PGKGDIPTYV VGVNEEGYTH ADTIISNASC TTNCLAPFVK VLDQKFGIIK GT MTTTHSY TGDQRLLDAS HRDLRRARAA CLNIVPTSTG AAKAVALVLP NLKGKLNGIA LRVPTPNVSV VDLVVQVSKK TFA EEVNAA FRESADNELK GILSVCDEPL VSIDFRCTDV SSTIDSSLTM VMGDDMVKVI AWYDNEWGYS QRVVDLADIV ANKW Q(UNK) |
-Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |