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- EMDB-52552: Photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (min... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52552
TitlePhotosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.
Map dataA8B8 photosynthetic GAPDH minor form cryo-EM map.
Sample
  • Complex: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Keywordsphotosynthesis / Calvin-Benson cycle / redox regulation / OXIDOREDUCTASE
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
Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMarotta R / Fermani S / Sparla F / Trost P / Del Giudice A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
iNEXT-Discovery22228European Union
CitationJournal: To Be Published
Title: Photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.
Authors: Marotta R / Fermani S / Sparla F
History
DepositionJan 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52552.png

Downloads & links

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Map

FileDownload / File: emd_52552.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA8B8 photosynthetic GAPDH minor form cryo-EM map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 412 pix.
= 301.172 Å		0.73 Å/pix.
x 412 pix.
= 301.172 Å		0.73 Å/pix.
x 412 pix.
= 301.172 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2786292 - 2.5024743
Average (Standard dev.)0.000024040042 (±0.060944457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 301.172 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: A8B8 photosynthetic GAPDH minor form cryo-EM half map.

Fileemd_52552_half_map_1.map
AnnotationA8B8 photosynthetic GAPDH minor form cryo-EM half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A8B8 photosynthetic GAPDH minor form cryo-EM half map.

Fileemd_52552_half_map_2.map
AnnotationA8B8 photosynthetic GAPDH minor form cryo-EM half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (...

EntireName: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
Components
  • Complex: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (...

SupramoleculeName: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Spinacia oleracea (spinach)

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

MacromoleculeName: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 39.403957 KDa
SequenceString: 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

UniProtKB: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic

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Macromolecule #2: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

MacromoleculeName: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 36.256391 KDa
SequenceString: 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

UniProtKB: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

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Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 16 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.6 mg/mL
BufferpH: 7.5 / Component - Concentration: 25.0 mM / Component - Formula: K2PO4 / Component - Name: potassium phosphate buffer / Details: 25 mM potassium phosphate buffer pH 7.5 1mM NAD
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: Using Gatan SOLARUS plasma cleaner.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.65 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification carried out in conventional atmosphere..
DetailsThe sample contained several photosynthetic AB-GAPDH oligomers.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
DetailsPreliminary grid screening was performed on a FEI Tecnai G2 F20 TEM equipped with cryo-box and direct electron detector.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 16384 pixel / Digitization - Dimensions - Height: 16384 pixel / Number grids imaged: 5 / Number real images: 23000 / Average electron dose: 40.0 e/Å2
Details: The images were corrected in movie mode. Each movie contained 702 EER frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were motion-corrected, ctf-corrected, and normalized.
Particle selectionNumber selected: 3156722
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ellipsoid as an unbiased initial model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Details: RELION was used for the reconstruction. / Number images used: 57847
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 8
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2pkq


Chain - Chain ID: RSPQ / Chain - Residue range: 1-2115 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model was obtained starting from the complete biological assembly for PDB entry 2PKQ.
DetailsInitial local fitting was done using 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9i06:
Photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

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