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- EMDB-63281: Cryo-EM structure of rice PHS1-DPE1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63281
TitleCryo-EM structure of rice PHS1-DPE1 complex
Map data
Sample
  • Complex: Rice PHS1-DPE1 complex protomer II
    • Protein or peptide: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
    • Protein or peptide: Alpha-1,4 glucan phosphorylase
KeywordsComplex / Starch biosynthersis / Rice / Maltooligosaccharide elongation / 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 / 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 subsp. japonica (Rice) (Japanese rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.4 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: To Be Published
Title: Cryo-EM structure of rice PHS1-DPE1 complex protomer II
Authors: Liu J / Yan J
History
DepositionJan 26, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63281.png

Downloads & links

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Map

FileDownload / File: emd_63281.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.9454997 - 1.5246019
Average (Standard dev.)-0.0009680849 (±0.039926875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63281_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63281_half_map_2.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 : Rice PHS1-DPE1 complex protomer II

EntireName: Rice PHS1-DPE1 complex protomer II
Components
  • Complex: Rice PHS1-DPE1 complex protomer II
    • Protein or peptide: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
    • Protein or peptide: Alpha-1,4 glucan phosphorylase

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Supramolecule #1: Rice PHS1-DPE1 complex protomer II

SupramoleculeName: Rice PHS1-DPE1 complex protomer II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 / Number of copies: 2 / Enantiomer: LEVO / EC number: 4-alpha-glucanotransferase
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 66.360562 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 EFRIDHFRGL 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: 109.299164 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 FDVQVKRIHE 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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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.07 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris-HCl 8.0
150.0 mMNaClNaCl
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details1.07 mg/ml complex

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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: 1160 / Average electron dose: 50.0 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: 1.8 µm / Nominal defocus min: 1.2 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: 1077846
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 27 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 243835
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)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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