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- EMDB-67288: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67288
TitleMaltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer
Map data
Sample
  • Complex: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer
    • Protein or peptide: Isoamylase 1, chloroplastic
Keywordsisoamylase / ISA1 / ISA2 / PLANT PROTEIN
Function / homology
Function and homology information


chloroplast isoamylase complex / isoamylase / isoamylase activity / amylopectin biosynthetic process / starch biosynthetic process / starch catabolic process / chloroplast
Similarity search - Function
: / 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 ...: / 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
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: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer
Authors: Wang RY / Lin HJ / Fan MR
History
DepositionNov 26, 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_67288.png

Downloads & links

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Map

FileDownload / File: emd_67288.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: 0.27
Minimum - Maximum-1.5638582 - 2.3908324
Average (Standard dev.)-0.000064767155 (±0.043936122)
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_67288_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67288_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67288_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-incubated Arabidopsis ISA1-ISA1 homodimer

EntireName: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer
Components
  • Complex: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer
    • Protein or peptide: Isoamylase 1, chloroplastic

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Supramolecule #1: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer

SupramoleculeName: Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer
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: 89.311125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DAKDRRSNEA ENIAVVEKPL KSDRFFISDG LPSPFGPTVR DDGVNFSVY STNSVSATIC LISLSDLRQN KVTEEIQLDP SRNRTGHVWH VFLRGDFKDM LYGYRFDGKF SPEEGHYYDS S NILLDPYA ...String:
MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DAKDRRSNEA ENIAVVEKPL KSDRFFISDG LPSPFGPTVR DDGVNFSVY STNSVSATIC LISLSDLRQN KVTEEIQLDP SRNRTGHVWH VFLRGDFKDM LYGYRFDGKF SPEEGHYYDS S NILLDPYA KAIISRDEFG VLGPDDNCWP QMACMVPTRE EEFDWEGDMH LKLPQKDLVI YEMHVRGFTR HESSKIEFPG TY QGVAEKL DHLKELGINC IELMPCHEFN ELEYYSYNTI LGDHRVNFWG YSTIGFFSPM IRYASASSNN FAGRAINEFK ILV KEAHKR GIEVIMDVVL NHTAEGNEKG PIFSFRGVDN SVYYMLAPKG EFYNYSGCGN TFNCNHPVVR QFILDCLRYW VTEM HVDGF RFDLGSIMSR SSSLWDAANV YGADVEGDLL TTGTPISCPP VIDMISNDPI LRGVKLIAEA WDAGGLYQVG MFPHW GIWS EWNGKFRDVV RQFIKGTDGF SGAFAECLCG SPNLYQGGRK PWHSINFICA HDGFTLADLV TYNNKNNLAN GEENND GEN HNYSWNCGEE GDFASISVKR LRKRQMRNFF VSLMVSQGVP MIYMGDEYGH TKGGNNNTYC HDNYMNYFRW DKKEEAH SD FFRFCRILIK FRDECESLGL NDFPTAKRLQ WHGLAPEIPN WSETSRFVAF SLVDSVKKEI YVAFNTSHLA TLVSLPNR P GYRWEPFVDT SKPSPYDCIT PDLPERETAM KQYRHFLDAN VYPMLSYSSI ILLLSPIKDP

UniProtKB: Isoamylase 1, 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: 300 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: 194545
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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