2026-01-21 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-01-14 2026-01-21 2026-01-21 2026-01-21 iNEXT-Discovery 22228 European Union Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea. Marotta R Fermani S Sparla F photosynthesis, Calvin-Benson cycle, redox regulation, OXIDOREDUCTASE Marotta R Fermani S Sparla F Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea. To Be Published 0353 EMD-13826 other EM volume
Previous lower resolution cryo electron density map for the the photosynthetic A8B8 GAPDH (major form)oligomer
 9i07 FULLOVERLAP PDB 2PKQ unspecified
Initial crystallografic model
 PDB 7Q55 unspecified
Previous lower resolution model for the photosynthetic A8B8 GAPDH (major form) oligomer
 EMDB EMD-13826 other EM volume
Previous lower resolution cryo electron density map for the the photosynthetic A8B8 GAPDH (major form)oligomer
 EMDB EMD-52553 associated EM volume
Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea.
 A8B8 photosynthetic glyceraldeyde 3-phospahte dehydrogenase hetero-hexadecamer (major conformer) complexed with NAD A8B8 photosynthetic glyceraldeyde 3-phospahte dehydrogenase hetero-hexadecamer (major conformer) complexed with NAD 0 1 2 Spinacia oleracea Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic Spinacia oleracea 0.039403957 8 LEVO KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKSATHLLKYDSILGTFKADVKIIDNETFSIDGKPIKVVSNR DPLKLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVIITAPAKGSDIPTYVVGVNEKDYGHDVANIISNASCTTNCL APFVKVLDEELGIVKGTMTTTHSYTGDQRLLDASHRDLRRARAAALNIVPTSTGAAKAVSLVLPQLKGKLNGIALRVPTP NVSVVDLVVNIEKVGVTAEDVNNAFRKAAAGPLKGVLDVCDIPLVSVDFRCSDFSSTIDSSLTMVMGGDMVKVVAWYDNE WGYSQRVVDLADLVANKWPGLEGSVASGDPLEDFCKDNPADEECKLYE P12860 Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic Spinacia oleracea 0.036256391 8 LEVO KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVINDTGGVKQASHLLKYDSILGTFDADVKTAGDSAISVDGKVIKVVSDR NPVNLPWGDMGIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAPGKGDIPTYVVGVNEEGYTHADTIISNASCTTNCLAP FVKVLDQKFGIIKGTMTTTHSYTGDQRLLDASHRDLRRARAACLNIVPTSTGAAKAVALVLPNLKGKLNGIALRVPTPNV SVVDLVVQVSKKTFAEEVNAAFRESADNELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTMVMGDDMVKVIAWYDNEWGY SQRVVDLADIVANKWQA P19866 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 0.0006634249999999999 16 NAD singleParticle particle 1.6 7.5 25.0 K2PO4 potassium phosphate buffer
25 mM potassium phosphate buffer pH 7.5 1mM NAD
 C-flat-1.2/1.3 COPPER 300 CARBON HOLEY PLASMA CLEANING AIR ETHANE 100 277.65 FEI VITROBOT MARK IV
Vitrification carried out in conventional atmosphere..
This sample contained several photosynthetic AB-GAPDH oligomers.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 1.5 3.0 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris
Preliminary grid screening was perfomed manually on a FEI Tecnai G2 F20 TEM equipped with cryo-box and direct electron detector.
FEI FALCON IV (4k x 4k) 16384 16384 5 23000 40.0
The images were collected in movie mode. Each movie contains 702 EER frames.
 1
The selected images were motion-corrected, ctf-corrected, and normalized.
3156722 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION
Ellipsoid as an unbiased initial model
 1 C2 BACK PROJECTION 3.1 FSC 0.143 CUT-OFF RELION 4.0
RELION was used for the reconstruction.
55141 PROJECTION MATCHING PROJECTION MATCHING 8 emd_52553.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 412 412 412 0 0 0 412 412 412 301.172 301.172 301.172 90.0 90.0 90.0 Z Y X -1.3738972 2.2831402 0.000022303624 0.0649819 0.731 0.731 0.731 0.2 AUTHOR GAPDH A8B8 major conformer cryo-EM map. 2PKQ RSPQ 1-2115 PDB experimental model
The initial model was obtained starting from the complete biological assembly for PDB entry 2PKQ.
 RIGID BODY FIT
Initial local fitting was done unsing 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.
Cross-correlation coefficient REAL emd_52553_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 412 412 412 0 0 0 412 412 412 301.172 301.172 301.172 90.0 90.0 90.0 X Y Z -0.015433118 0.035791963 0.0002026486 0.0023591544 0.731 0.731 0.731 AUTHOR GAPDH A8B8 major conformer cryo-EM half map. emd_52553_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 412 412 412 0 0 0 412 412 412 301.172 301.172 301.172 90.0 90.0 90.0 X Y Z -0.0152563555 0.03684796 0.0002020022 0.002363709 0.731 0.731 0.731 AUTHOR GAPDH A8B8 major conformer cryo-EM half map.