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- EMDB-67303: Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67303
TitleMaltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer
Map data
Sample
  • Complex: Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer
    • Protein or peptide: Isoamylase 1, chloroplastic
    • Protein or peptide: Isoamylase 2, chloroplastic
Keywordsisoamylase / ISA1 / ISA2 / PLANT PROTEIN
Function / homology
Function and homology information


isoamylase complex / chloroplast isoamylase complex / isoamylase / isoamylase activity / amylopectin biosynthetic process / starch biosynthetic process / starch catabolic process / chloroplast
Similarity search - Function
Isoamylase 2, catalytic domain / : / Isoamylase 1-3, C-terminal / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta ...Isoamylase 2, catalytic domain / : / Isoamylase 1-3, C-terminal / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Isoamylase 1, chloroplastic / Isoamylase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsWang RY / Lin HJ / Fan MR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: Arabidopsis ISA2-ISA1-ISA1 heterotrimer
Authors: Wang RY / Lin HJ / Fan MR
History
DepositionNov 27, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67303.png

Downloads & links

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Map

FileDownload / File: emd_67303.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.)
0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.9727291 - 2.717943
Average (Standard dev.)-0.0002977904 (±0.05300059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67303_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67303_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_67303_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 : Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer

EntireName: Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer
Components
  • Complex: Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer
    • Protein or peptide: Isoamylase 1, chloroplastic
    • Protein or peptide: Isoamylase 2, chloroplastic

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Supramolecule #1: Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer

SupramoleculeName: Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Isoamylase 1, chloroplastic

MacromoleculeName: Isoamylase 1, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: isoamylase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 87.301906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAHHHHHHHH HHGSGSGSGS GSEFAKDRRS NEAENIAVVE KPLKSDRFFI SDGLPSPFGP TVRDDGVNFS VYSTNSVSAT ICLISLSDL RQNKVTEEIQ LDPSRNRTGH VWHVFLRGDF KDMLYGYRFD GKFSPEEGHY YDSSNILLDP YAKAIISRDE F GVLGPDDN ...String:
MAHHHHHHHH HHGSGSGSGS GSEFAKDRRS NEAENIAVVE KPLKSDRFFI SDGLPSPFGP TVRDDGVNFS VYSTNSVSAT ICLISLSDL RQNKVTEEIQ LDPSRNRTGH VWHVFLRGDF KDMLYGYRFD GKFSPEEGHY YDSSNILLDP YAKAIISRDE F GVLGPDDN CWPQMACMVP TREEEFDWEG DMHLKLPQKD LVIYEMHVRG FTRHESSKIE FPGTYQGVAE KLDHLKELGI NC IELMPCH EFNELEYYSY NTILGDHRVN FWGYSTIGFF SPMIRYASAS SNNFAGRAIN EFKILVKEAH KRGIEVIMDV VLN HTAEGN EKGPIFSFRG VDNSVYYMLA PKGEFYNYSG CGNTFNCNHP VVRQFILDCL RYWVTEMHVD GFRFDLGSIM SRSS SLWDA ANVYGADVEG DLLTTGTPIS CPPVIDMISN DPILRGVKLI AEAWDAGGLY QVGMFPHWGI WSEWNGKFRD VVRQF IKGT DGFSGAFAEC LCGSPNLYQG GRKPWHSINF ICAHDGFTLA DLVTYNNKNN LANGEENNDG ENHNYSWNCG EEGDFA SIS VKRLRKRQMR NFFVSLMVSQ GVPMIYMGDE YGHTKGGNNN TYCHDNYMNY FRWDKKEEAH SDFFRFCRIL IKFRDEC ES LGLNDFPTAK RLQWHGLAPE IPNWSETSRF VAFSLVDSVK KEIYVAFNTS HLATLVSLPN RPGYRWEPFV DTSKPSPY D CITPDLPERE TAMKQYRHFL DANVYPMLSY SSIILLLSPI KDP

UniProtKB: Isoamylase 1, chloroplastic

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Macromolecule #2: Isoamylase 2, chloroplastic

MacromoleculeName: Isoamylase 2, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 97.595516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DGDLVTSALQ SYQFSKICAS KTSIELREAL SSRRAEADDL KKVTSYSFR TKAGALVKVK VEKKREKYSI LVYVSSLELS GDDKSRLVMV WGVYRSDSSC FLPLDFENSS QDSQTHTTET T FVKSSLSE ...String:
MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DGDLVTSALQ SYQFSKICAS KTSIELREAL SSRRAEADDL KKVTSYSFR TKAGALVKVK VEKKREKYSI LVYVSSLELS GDDKSRLVMV WGVYRSDSSC FLPLDFENSS QDSQTHTTET T FVKSSLSE LMLGLEFDGK ESPFYLSFHL KLVSGRDPDG QEMLTHRDTD FCIPVGFTAG HPLPLGLSSG PDDDSWNFSF FS RSSTNVV LCLYDDSTTD KPALELDLDP YVNRTGDVWH ASVDNTWDFV RYGYRCKETA HSKEDVDVEG EPIVLDPYAT VVG KSVSQK YLGSLSKSPS FDWGEDVSPN IPLEKLLVYR LNVKGFTQHR SSKLPSNVAG TFSGVAEKVS HLKTLGTNAV LLEP IFSFS EQKGPYFPFH FFSPMDIYGP SNSLESAVNS MKVMVKKLHS EGIEVLLEVV FTHTADSGAL RGIDDSSYYY KGRAN DLDS KSYLNCNYPV VQQLVLESLR YWVTEFHVDG FCFINASSLL RGVHGEQLSR PPLVEAIAFD PLLAETKLIA DCWDPL EMM PKEVRFPHWK RWAELNTRYC RNVRNFLRGR GVLSDLATRI CGSGDVFTDG RGPAFSFNYI SRNSGLSLVD IVSFSGP EL ASELSWNCGE EGATNKSAVL QRRLKQIRNF LFIQYISLGV PVLNMGDECG ISTRGSPLLE SRKPFDWNLL ASAFGTQI T QFISFMTSVR ARRSDVFQRR DFLKPENIVW YANDQTTPKW EDPASKFLAL EIKSESEEEE TASLAEPNEP KSNDLFIGF NASDHPESVV LPSLPDGSKW RRLVDTALPF PGFFSVEGET VVAEEPLQQL VVYEMKPYSC TLFETINTTA

UniProtKB: Isoamylase 2, chloroplastic

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 459616
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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