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- EMDB-63699: cryo-EM structure of maltose and glucose bound rice PHS1(R709A)-D... -

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Basic information

Entry
Database: EMDB / ID: EMD-63699
Titlecryo-EM structure of maltose and glucose bound rice PHS1(R709A)-DPE1(D391A) complex
Map data
Sample
  • Complex: maltopentaose incubated PHS1(R709A)-DPE1(D391A) complex
    • Protein or peptide: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
    • Protein or peptide: Alpha-1,4 glucan phosphorylase
  • Ligand: alpha-D-glucopyranose
KeywordsComplex / Starch biosynthersis / Rice / Maltooligosaccharide elongation / inactive mutant / TRANSFERASE
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 / 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 subsp. japonica (Rice) (Japanese rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.07 Å
AuthorsLiu J / Yan J
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400216 China
National Natural Science Foundation of China (NSFC)32270255 China
CitationJournal: Nat Commun / Year: 2026
Title: The plastidial PHS1-DPE1 complex drives efficient malto-oligosaccharides synthesis in rice starch metabolism.
Authors: Jian Liu / Xinru Wu / Haitao He / Xi Yang / Yuanhuai Hu / Fei Zhang / Rong Fan / Xuecui Wang / Shenao Yang / Lian Xiong / Delin Zhang / Ping Yin / Jianping Guo / Zhu Liu / Junjie Yan /
Abstract: Starch serves as a vital energy reserve in plants. During its biosynthesis, malto-oligosaccharides (MOS) are essential primers. One of the key pathways for MOS production involves plastidial α- ...Starch serves as a vital energy reserve in plants. During its biosynthesis, malto-oligosaccharides (MOS) are essential primers. One of the key pathways for MOS production involves plastidial α-glucan phosphorylase (PHS1/Pho1) and disproportionating enzyme (DPE1). However, the functional relationship between these enzymes is unclear. Here, we demonstrate that rice PHS1 and DPE1 assemble into a multimeric complex. Cryo-EM structures of the PHS1-DPE1 complex reveal an assembly mechanism and suggest a potential substrate tunnel. Biochemical assays show the complex dramatically enhances catalytic efficiency over individual enzymes. Single-molecule fluorescence resonance energy transfer (smFRET) visualizes conformational dynamics, enabling rapid substrate transfer between the enzymes. We further identify the unique L80 loop in PHS1 as a potential regulator. Its deletion reduces catalytic efficiency and prolongs conformational state lifetimes during substrate transfer, thereby reducing the production of longer MOSs. Our findings establish that the PHS1-DPE1 complex facilitates efficient MOS primer synthesis through efficient substrate transfer or diffusion between the two enzymes, providing mechanistic insight into a critical step of starch biosynthesis with agronomic implications.
History
DepositionMar 11, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63699.png

Downloads & links

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Map

FileDownload / File: emd_63699.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 316.416 Å		0.82 Å/pix.
x 384 pix.
= 316.416 Å		0.82 Å/pix.
x 384 pix.
= 316.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-2.3928552 - 3.0210915
Average (Standard dev.)-0.00033291563 (±0.07301246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : maltopentaose incubated PHS1(R709A)-DPE1(D391A) complex

EntireName: maltopentaose incubated PHS1(R709A)-DPE1(D391A) complex
Components
  • Complex: maltopentaose incubated PHS1(R709A)-DPE1(D391A) complex
    • Protein or peptide: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
    • Protein or peptide: Alpha-1,4 glucan phosphorylase
  • Ligand: alpha-D-glucopyranose

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Supramolecule #1: maltopentaose incubated PHS1(R709A)-DPE1(D391A) complex

SupramoleculeName: maltopentaose incubated PHS1(R709A)-DPE1(D391A) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryza sativa subsp. japonica (Rice) (Japanese rice)
Location in cell: chloroplast

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Macromolecule #1: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic

MacromoleculeName: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
type: protein_or_peptide / ID: 1 / Details: D391A / Number of copies: 2 / Enantiomer: LEVO / EC number: 4-alpha-glucanotransferase
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 66.316555 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MATLSLPLPH LTQAIPARAR PRPRPLRGIP ARLLSCRAAM AVAPDKEEAA AVALDKAVKV AVAAPDRAAV AAVGVGEELP EGYDQMMPA VEEARRRRAG VLLHPTSLRG PHGIGDLGDE AVAFLAWLRD AGCTLWQVLP LVPPGRKSGE DGSPYSGQDA N CGNTLLIS ...String:
MATLSLPLPH LTQAIPARAR PRPRPLRGIP ARLLSCRAAM AVAPDKEEAA AVALDKAVKV AVAAPDRAAV AAVGVGEELP EGYDQMMPA VEEARRRRAG VLLHPTSLRG PHGIGDLGDE AVAFLAWLRD AGCTLWQVLP LVPPGRKSGE DGSPYSGQDA N CGNTLLIS LEELVKDGLL MENELPDPLD MEYVEFDTVA NLKEPLIAKA AERLLLSRGE LRTQYDCFKK NPNISGWLED AA LFAAIDR SIDALSWYEW PEPLKNRHLR ALEDIYQKQK DFIEIFMAQQ FLFQRQWQRI RKYAKKLGIS IMGDMPIYVG YHS ADVWAN RKSFLLDKNG FPTFVSGVPP DAFSETGQLW NSPLYDWKAM EAGGFEWWIK RINRALDLYD EFRIAHFRGL AGFW AVPSE SKVALVGSWR AGPRNAFFDA LFKAVGRINI IAEDLGVITE DVVDLRKSIE APGMAVLQFA FGGGSDNPHL PHNHE FDQV VYTGTHDNDT VIGWWQTLPE EEKQTVFKYL PEANRTEISW ALITAALSSV ARTSMVTMQD ILGLDSSARM NTPATQ KGN WRWRMPSSVS FDSLSPEAAK LKELLGLYNR L

UniProtKB: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic

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Macromolecule #2: Alpha-1,4 glucan phosphorylase

MacromoleculeName: Alpha-1,4 glucan phosphorylase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycogen phosphorylase
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 109.213047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MATASAPLQL ATASRPLPVG VGCGGGGGGG LHVGGARGGG AAPARRRLAV RSVASDRGVQ GSVSPEEEIS SVLNSIDSST IASNIKHHA EFTPVFSPEH FSPLKAYHAT AKSVLDTLIM NWNATYDYYD RTNVKQAYYL SMEFLQGRAL TNAVGNLELT G QYAEALQQ ...String:
MATASAPLQL ATASRPLPVG VGCGGGGGGG LHVGGARGGG AAPARRRLAV RSVASDRGVQ GSVSPEEEIS SVLNSIDSST IASNIKHHA EFTPVFSPEH FSPLKAYHAT AKSVLDTLIM NWNATYDYYD RTNVKQAYYL SMEFLQGRAL TNAVGNLELT G QYAEALQQ LGHSLEDVAT QEPDAALGNG GLGRLASCFL DSLATLNYPA WGYGLRYKHG LFKQIITKDG QEEVAENWLE MG NPWEIVR TDVSYPVKFY GKVVEGTDGR MHWIGGENIK VVAHDIPIPG YKTKTTNNLR LWSTTVPSQD FDLEAFNAGD HAS AYEAHL NAEKICHVLY PGDESPEGKV LRLKQQYTLC SASLQDIIAR FERRAGDSLS WEDFPSKVAV QMNDTHPTLC IPEL MRILI DVKGLSWNEA WSITERTVAY TNHTVLPEAL EKWSLDIMQK LLPRHVEIIE KIDGELMNII ISKYGTEDTS LLKKK IKEM RILDNIDLPD SIAKLFVKPK EKKESPAKLK EKLLVKSLEP SVVVEEKTVS KVEINEDSEE VEVDSEEVVE AENEDS EDE LDPFVKSDPK LPRVVRMANL CVVGGHSVNG VAAIHSEIVK EDVFNSFYEM WPAKFQNKTN GVTPRRWIRF CNPELSA II SKWIGSDDWV LNTDKLAELK KFADDEDLQS EWRAAKKANK VKVVSLIREK TGYIVSPDAM FDVQVKAIHE YKRQLLNI L GIVYRYKKMK EMSAKDRINS FVPRVCIFGG KAFATYVQAK RIVKFITDVA ATVNHDPEIG DLLKVVFIPD YNVSVAEAL IPASELSQHI STAGMEASGT SNMKFAMNGC ILIGTLDGAN VEIREEVGEE NFFLFGAEAH EIAGLRKERA QGKFVPDPRF EEVKRFVRS GVFGTYNYDD LMGSLEGNEG YGRADYFLVG KDFPSYIECQ EKVDKAYRDQ KLWTRMSILN TASSSKFNSD R TIHEYAKD IWDIKPVILP

UniProtKB: Alpha-1,4 glucan phosphorylase

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Macromolecule #4: alpha-D-glucopyranose

MacromoleculeName: alpha-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: GLC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GLC:
alpha-D-glucopyranose

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.08 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris-HCl 8.0
150.0 mMNaClNaCl
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details1.08 mg/ml inactive complex incubated with 5 mM maltopentaose

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1936 / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2236025
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 21 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 116368
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 83.5
Output model

PDB-9m80:
cryo-EM structure of maltose and glucose bound rice PHS1(R709A)-DPE1(D391A) complex

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