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- PDB-9lpz: Cryo-EM structure of rice PHS1-DPE1 complex -

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Basic information

Entry
Database: PDB / ID: 9lpz
TitleCryo-EM structure of rice PHS1-DPE1 complex
Components
  • 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
  • Alpha-1,4 glucan phosphorylase
KeywordsTRANSFERASE / Complex / Starch biosynthersis / Rice / Maltooligosaccharide elongation
Function / homology
Function and homology information


amyloplast / maltose catabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / starch catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / polysaccharide catabolic process / chloroplast / glucose metabolic process ...amyloplast / maltose catabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / starch catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / polysaccharide catabolic process / chloroplast / glucose metabolic process / pyridoxal phosphate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase / 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 2.4 Å
AuthorsLiu, J. / Yan, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400216 China
National Natural Science Foundation of China (NSFC)32270255 China
CitationJournal: To Be Published
Title: Cryo-EM structure of rice PHS1-DPE1 complex protomer II
Authors: Liu, J. / Yan, J.
History
DepositionJan 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 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: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
D: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
B: Alpha-1,4 glucan phosphorylase
C: Alpha-1,4 glucan phosphorylase


Theoretical massNumber of molelcules
Total (without water)351,3194
Polymers351,3194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic / Amylomaltase / Disproportionating enzyme / D-enzyme / Protein DISPROPORTIONATING ENZYME 1


Mass: 66360.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Rice
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: DPE1, Os07g0627000, LOC_Os07g43390, OJ1339_F05.134, P0506F02.102
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8LI30, 4-alpha-glucanotransferase
#2: Protein Alpha-1,4 glucan phosphorylase


Mass: 109299.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: pho1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3IYE3, glycogen phosphorylase
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: Rice PHS1-DPE1 complex protomer II / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa subsp. japonica (Rice) (Japanese rice)
Cellular location: chloroplast
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HCl 8.0C4H11NO31
2150 mMNaClNaCl1
SpecimenConc.: 1.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES / Details: 1.07 mg/ml complex
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1160

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6.0particle selection
4cryoSPARC4.6.0CTF correction
7cryoSPARC4.6.0model fitting
9PHENIX1.21.2model refinement5419
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1077846
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243835 / Num. of class averages: 27 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422208
ELECTRON MICROSCOPYf_angle_d0.53530103
ELECTRON MICROSCOPYf_dihedral_angle_d4.452950
ELECTRON MICROSCOPYf_chiral_restr0.0433249
ELECTRON MICROSCOPYf_plane_restr0.0043888

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