9J6X | pdb_00009j6x

Cryo-EM structure of the rice isoamylase ISA1-ISA2 heterocomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9J6X

This is version 1.2 of the entry. See complete history

Literature

Amylopectin branch trimming and biosynthesis elucidated by the rice isoamylase ISA1-ISA2 heterocomplex.

Fan, R.Guan, Z.Zhou, G.Yang, X.Zhang, F.Wu, M.Wang, X.Liu, J.Chen, P.Liu, Y.Zhang, D.Yin, P.Yan, J.

(2025) Nat Commun 16: 5638-5638

  • DOI: https://doi.org/10.1038/s41467-025-60944-6
  • Primary Citation Related Structures: 
    9J60, 9J6X, 9LFN

  • PubMed Abstract: 

    Amylopectin, the primary form of starch in plant leaves, seeds and tubers, features a tree-like architecture with branched glucose chains. Excess branches result in the formation of soluble phytoglycogen instead of starch granules. In higher plants and green algae, the debranching enzyme isoamylase ISA1 forms either homomultimer or hetero-multimer with ISA2 to facilitate branch trimming and starch granule formation, but the molecular basis remains largely unknown. In this study, we reconstitute the rice OsISA1-ISA2 complex in vitro and determine the cryo-EM structures of the OsISA1 homodimer, as well as the malto-oligosaccharide (MOS)-free and MOS-bound OsISA1-ISA2 heterocomplex. The OsISA1 dimer shows a tail-to-tail rod-like architecture, whereas the OsISA1-ISA2 complex mainly exhibits as a trimer, with OsISA2 flanking on the N-terminal segments of the dimeric OsISA1. Combined with comprehensive biochemical analyses, these structural data elucidate the organization of the ISA1-ISA2 heterocomplex in higher plants and demonstrate how ISA1 and ISA2 cooperate during amylopectin biosynthesis.


  • Organizational Affiliation
    • National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 261.19 kDa 
  • Atom Count: 16,969 
  • Modeled Residue Count: 2,156 
  • Deposited Residue Count: 2,354 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoamylase 1, chloroplastic
A, B
777Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: ISA1ISASU1Os08g0520900LOC_Os08g40930
EC: 3.2.1.68
UniProt
Find proteins for D0TZF0 (Oryza sativa subsp. japonica)
Explore D0TZF0 
Go to UniProtKB:  D0TZF0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0TZF0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoamylase 2, chloroplastic800Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: ISA2Os05g0393700LOC_Os05g32710OsJ_17304OSJNBa0014C03.3
EC: 3.2.1.68
UniProt
Find proteins for Q6AU80 (Oryza sativa subsp. japonica)
Explore Q6AU80 
Go to UniProtKB:  Q6AU80
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6AU80
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection