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- PDB-9kz7: The cryo-EM structure of porcine serum MGAM bound with Acarviosyl... -

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Basic information

Entry
Database: PDB / ID: 9kz7
TitleThe cryo-EM structure of porcine serum MGAM bound with Acarviosyl-maltotriose.
ComponentsMaltase-glucoamylase
KeywordsHYDROLASE / alpha-glucosidase
Function / homology
Function and homology information


Digestion of dietary carbohydrate / dextrin catabolic process / maltose catabolic process / alpha-1,4-glucosidase activity / Neutrophil degranulation / carbohydrate binding / apical plasma membrane
Similarity search - Function
P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain ...P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Maltase-glucoamylase
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsTagami, T. / Kawasaki, M. / Adachi, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: J Enzyme Inhib Med Chem / Year: 2026
Title: Porcine serum maltase-glucoamylase: structure, kinetics, and inhibition
Authors: Watanabe, K. / Tagami, T. / Biwa, C. / Kawasaki, M. / Adachi, N. / Moriya, T. / Senda, T. / Okuyama, M.
History
DepositionDec 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltase-glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,10415
Polymers203,5101
Non-polymers6,59414
Water00
1


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

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Components

#1: Protein Maltase-glucoamylase


Mass: 203509.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / Strain: Duroc x Landrace x Large White / Tissue: serum / References: UniProt: A0A287A042
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 807.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2-2-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: porcine serum MGAM / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.351 MDa / Experimental value: YES
Source (natural)Organism: Sus scrofa (pig) / Strain: Duroc x Landrace x Large White / Tissue: serum
Buffer solutionpH: 6
Details: 20 mM Sodium acetate pH 6.0, 0.1 mM acarviosyl-maltotriose
Buffer componentConc.: 20 mM / Name: sodium acetate / Formula: CH3COONa
SpecimenConc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was washed by acetone prior to use. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blotting time was 5 seconds and blot force was 15.

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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 magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.58 sec. / Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6354
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13Servalcatmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2815507
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 607435 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingDetails: pre-determined apo form structure / Source name: Other / Type: other

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