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- PDB-9lfn: Cryo-EM structure of the rice isoamylase ISA1-ISA2 heterocomplex ... -

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Basic information

Entry
Database: PDB / ID: 9lfn
TitleCryo-EM structure of the rice isoamylase ISA1-ISA2 heterocomplex incubated with Amylopectin
Components
  • Isoamylase 1, chloroplastic
  • Isoamylase 2, chloroplastic
KeywordsHYDROLASE / isoamylase ISA1-ISA2
Function / homology
Function and homology information


chloroplast isoamylase complex / isoamylase / isoamylase complex / 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
alpha-D-glucopyranose / Isoamylase 1, chloroplastic / Isoamylase 2, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGuan, Z.Y. / Yan, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The tree-like architecture of the rice isoamylase ISA1-ISA2 heterocomplex facilitates branch trimming and amylopectin synthesis
Authors: Guan, Z.Y. / Yan, J.J.
History
DepositionJan 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoamylase 1, chloroplastic
B: Isoamylase 1, chloroplastic
C: Isoamylase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,77016
Polymers261,1853
Non-polymers5,58513
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoamylase 1, chloroplastic / OsISA1 / Protein SUGARY-1


Mass: 87281.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: ISA1, ISA, SU1, Os08g0520900, LOC_Os08g40930 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0TZF0, isoamylase
#2: Protein Isoamylase 2, chloroplastic / OsISA2


Mass: 86622.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: ISA2, Os05g0393700, LOC_Os05g32710, OsJ_17304, OSJNBa0014C03.3
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6AU80, isoamylase
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-Glucopyranose-(1-4)-alpha-L-Glucopyranose-(1-4)-alpha-L-Glucopyranose-(1-4)-alpha-D- ...alpha-L-Glucopyranose-(1-4)-alpha-L-Glucopyranose-(1-4)-alpha-L-Glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-L-Glcp]{[(4+1)][a-L-Glcp]{[(4+1)][a-L-Glcp]{}}}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SA1-ISA2-Amylopectin / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7315 / Symmetry type: POINT

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