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Yorodumi- EMDB-13827: Single Particle Cryo-EM structure of photosynthetic A8B8 glyceral... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13827 | |||||||||
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Title | Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea. | |||||||||
Map data | A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer | |||||||||
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 / apoplast / 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: 7.1 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_13827.map.gz | 13.7 MB | EMDB map data format | |
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Header (meta data) | emd-13827-v30.xml emd-13827.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13827_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_13827.png | 85.7 KB | ||
Others | emd_13827_half_map_1.map.gz emd_13827_half_map_2.map.gz | 79.3 MB 79.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13827 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13827 | HTTPS FTP |
-Validation report
Summary document | emd_13827_validation.pdf.gz | 695.3 KB | Display | EMDB validaton report |
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Full document | emd_13827_full_validation.pdf.gz | 694.8 KB | Display | |
Data in XML | emd_13827_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_13827_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13827 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13827 | HTTPS FTP |
-Related structure data
Related structure data | 7q56MC 7q53C 7q54C 7q55C 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_13827.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer | ||||||||||||||||||||||||||||||||||||
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: A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer -...
File | emd_13827_half_map_1.map | ||||||||||||
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Annotation | A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer -...
File | emd_13827_half_map_2.map | ||||||||||||
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Annotation | A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (...
Entire | Name: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD. |
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Components |
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-Supramolecule #1: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (...
Supramolecule | Name: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD. type: complex / 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: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: spinach (spinach) |
Molecular weight | Theoretical: 39.403957 KDa |
Sequence | String: KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVVNDSGGVK SATHLLKYDS ILGTFKADVK IIDNETFSID GKPIKVVSNR DPLKLPWAE LGIDIVIEGT GVFVDGPGAG KHIQAGAKKV IITAPAKGSD IPTYVVGVNE KDYGHDVANI ISNASCTTNC L APFVKVLD ...String: KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVVNDSGGVK SATHLLKYDS ILGTFKADVK IIDNETFSID GKPIKVVSNR DPLKLPWAE LGIDIVIEGT GVFVDGPGAG KHIQAGAKKV IITAPAKGSD IPTYVVGVNE KDYGHDVANI ISNASCTTNC L APFVKVLD EELGIVKGTM TTTHSYTGDQ RLLDASHRDL RRARAAALNI VPTSTGAAKA VSLVLPQLKG KLNGIALRVP TP NVSVVDL VVNIEKVGVT AEDVNNAFRK AAAGPLKGVL DVCDIPLVSV DFRCSDFSST IDSSLTMVMG GDMVKVVAWY DNE WGYSQR VVDLADLVAN KWPGLEGSVA SGDPLEDFCK DNPADEECKL YE |
-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: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: spinach (spinach) |
Molecular weight | Theoretical: 36.256391 KDa |
Sequence | String: KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVINDTGGVK QASHLLKYDS ILGTFDADVK TAGDSAISVD GKVIKVVSDR NPVNLPWGD MGIDLVIEGT GVFVDRDGAG KHLQAGAKKV LITAPGKGDI PTYVVGVNEE GYTHADTIIS NASCTTNCLA P FVKVLDQK ...String: KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVINDTGGVK QASHLLKYDS ILGTFDADVK TAGDSAISVD GKVIKVVSDR NPVNLPWGD MGIDLVIEGT GVFVDRDGAG KHLQAGAKKV LITAPGKGDI PTYVVGVNEE GYTHADTIIS NASCTTNCLA P FVKVLDQK FGIIKGTMTT THSYTGDQRL LDASHRDLRR ARAACLNIVP TSTGAAKAVA LVLPNLKGKL NGIALRVPTP NV SVVDLVV QVSKKTFAEE VNAAFRESAD NELKGILSVC DEPLVSIDFR CTDVSSTIDS SLTMVMGDDM VKVIAWYDNE WGY SQRVVD LADIVANKWQ A |
-Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 16 / 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 |