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- EMDB-13824: Single Particle Cryo-EM structure of photosynthetic A2B2 glyceral... -
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Open data
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Basic information
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Title | Single Particle Cryo-EM structure of photosynthetic A2B2 glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Marotta R / Fermani S / Sparla F / Trost P / Del Giudice A | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 2.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.5 KB | Display | ![]() |
Images | ![]() | 66.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q53MC ![]() 7q54C ![]() 7q55C ![]() 7q56C ![]() 7q57C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
-Entire : Photosynthetic A2B2 glyceraldehyde-3-phosphate dehydrogenase hete...
Entire | Name: Photosynthetic A2B2 glyceraldehyde-3-phosphate dehydrogenase hetero-tetramer complexed with NAD. |
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Components |
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-Supramolecule #1: Photosynthetic A2B2 glyceraldehyde-3-phosphate dehydrogenase hete...
Supramolecule | Name: Photosynthetic A2B2 glyceraldehyde-3-phosphate dehydrogenase hetero-tetramer complexed with NAD. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-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: 2 / Enantiomer: LEVO EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.28866 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 KWP |
-Macromolecule #2: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glycera...
Macromolecule | Name: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3- ...Name: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
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: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ![]() ChemComp-NAD: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |