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- PDB-9i3s: Photosynthetic A10B10 glyceraldehyde-3-phospahte dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 9i3s
TitlePhotosynthetic A10B10 glyceraldehyde-3-phospahte dehydrogenase from Spinacia oleracea.
Components
  • Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
  • Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
KeywordsOXIDOREDUCTASE / Photosynthesis / Calvin-Benson cycle / redox regulation
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
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsMarotta, R. / Fermani, S. / Sparla, F. / Del Giudice, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery22228European Union
CitationJournal: To Be Published
Title: Photosynthetic A10B10 glyceraldehyde-3-phospahte dehydrogenase from Spinacia oleracea.
Authors: Marotta, R. / Fermani, S. / Sparla, F.
History
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
B: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
C: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
D: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
E: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
G: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
H: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
I: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
J: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
K: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
L: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
M: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
N: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
S: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
T: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
O: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
P: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Q: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)769,87240
Polymers756,60320
Non-polymers13,26920
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Negative staining clearly shows the presence of the A10B10 oligomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic


Mass: 39403.957 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12860
#2: Protein
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic


Mass: 36256.391 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P19866
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A10B10 glyceraldehyde-3-phospahte dehydrogenase hetero-icosamer complexed with NAD.
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 7.5 / Details: 25 mM potassium phosphate buffer pH 7.5 1mM NAD
Buffer componentConc.: 25 mM / Name: potassium phosphate buffer / Formula: K2PO4
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample contained several photosynthetic AB-GAPDH oligomers.
Specimen supportDetails: Using GATAN SOLARUS plasma cleaner. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.65 K
Details: Vitrification carried out in conventional atmosphere.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Preliminary grid screening was performed on a FEI Tecnai G2 F20 TEM equipped with cryo-box and direct electron detector.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 23000
Details: The images were corrected in movie mode. Each movie contained 702 EER frames.
EM imaging opticsEnergyfilter name: TFS Selectris
Image scansWidth: 16384 / Height: 16384

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Processing

EM software
IDNameVersionCategoryDetails
1RELION4particle selection
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX1.7model fitting
12RELION43D reconstruction
13PHENIX1.2model refinementreal space refinement
Image processingDetails: The selected images were motion-corrected, ctf-corrected, and normalized.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3156722
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26638 / Algorithm: BACK PROJECTION / Details: RELION was used for the reconstruction. / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Initial local fitting was done suing ChimeraX starting from the crystallographic model PDB ID 2PKQ. Refinement was obtained trough several iterative cycles of COOT manual adjustment and ...Details: Initial local fitting was done suing ChimeraX starting from the crystallographic model PDB ID 2PKQ. Refinement was obtained trough several iterative cycles of COOT manual adjustment and Phenix real space refinement.
Atomic model buildingPDB-ID: 2PKQ

2pkq


Pdb chain-ID: RSPQ / Accession code: 2PKQ / Chain residue range: 1-2115
Details: The initial model consisted of the complete biological assembly for PDB entry 7Q57
Pdb chain residue range: 1-2115 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00454868
ELECTRON MICROSCOPYf_angle_d0.67874724
ELECTRON MICROSCOPYf_dihedral_angle_d6.4447818
ELECTRON MICROSCOPYf_chiral_restr0.0478850
ELECTRON MICROSCOPYf_plane_restr0.0059498

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