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- PDB-9xur: ADPG-bound ADP-Glucose Pyrophosphorylase -

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Basic information

Entry
Database: PDB / ID: 9xur
TitleADPG-bound ADP-Glucose Pyrophosphorylase
Components
  • Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
  • Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
KeywordsPLANT PROTEIN / heterotetramer / ADPG / amylosynthesis
Function / homology
Function and homology information


heterotetrameric ADPG pyrophosphorylase complex / glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / starch biosynthetic process / photoperiodism, flowering / apoplast / chloroplast envelope / glycogen biosynthetic process / chloroplast stroma ...heterotetrameric ADPG pyrophosphorylase complex / glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / starch biosynthetic process / photoperiodism, flowering / apoplast / chloroplast envelope / glycogen biosynthetic process / chloroplast stroma / plastid / chloroplast / ATP binding
Similarity search - Function
GLGC left-handed parallel beta-helix domain / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / Nucleotidyl transferase domain / Nucleotidyl transferase / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic / Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsWu, Y.T. / Lin, H.J. / Fan, M.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: ADPG-bound ADP-Glucose Pyrophosphorylase
Authors: Wu, Y.T. / Lin, H.J. / Fan, M.R.
History
DepositionNov 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
B: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
C: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
D: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,30316
Polymers208,1054
Non-polymers3,19912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic / ADP-glucose pyrophosphorylase / ADP-glucose synthase / AGPase B / Alpha-D-glucose-1-phosphate ...ADP-glucose pyrophosphorylase / ADP-glucose synthase / AGPase B / Alpha-D-glucose-1-phosphate adenyl transferase


Mass: 51517.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: APS1, ADG1, APS, At5g48300, K23F3.2 / Production host: Escherichia coli (E. coli)
References: UniProt: P55228, glucose-1-phosphate adenylyltransferase
#2: Protein Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic / ADP-glucose pyrophosphorylase / ADP-glucose synthase / AGPase S / Alpha-D-glucose-1-phosphate ...ADP-glucose pyrophosphorylase / ADP-glucose synthase / AGPase S / Alpha-D-glucose-1-phosphate adenyl transferase


Mass: 52535.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADG2, APL1, At5g19220, T24G5.120 / Production host: Escherichia coli (E. coli)
References: UniProt: P55229, glucose-1-phosphate adenylyltransferase
#3: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADQ / ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 589.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: ADPG-bound ADP-Glucose Pyrophosphorylase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1285715 / Symmetry type: POINT
RefinementHighest resolution: 2.49 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314144
ELECTRON MICROSCOPYf_angle_d0.48419178
ELECTRON MICROSCOPYf_dihedral_angle_d5.2431944
ELECTRON MICROSCOPYf_chiral_restr0.0462144
ELECTRON MICROSCOPYf_plane_restr0.0032464

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