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- PDB-9m9p: Glycogen phosphorylase dimer from E. coli -

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Basic information

Entry
Database: PDB / ID: 9m9p
TitleGlycogen phosphorylase dimer from E. coli
ComponentsAlpha-1,4 glucan phosphorylase
KeywordsSTRUCTURAL PROTEIN / glycogen metabolism / cryo-EM / gut bacteria
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsTakai, M. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural and mechanistic diversity of glycogen phosphrylases from gut bacteria
Authors: Shobu, K. / Takai, M. / Fukuda, Y. / Inoue, T.
History
DepositionMar 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data 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: Alpha-1,4 glucan phosphorylase


Theoretical massNumber of molelcules
Total (without water)95,5531
Polymers95,5531
Non-polymers00
Water00
1
A: Alpha-1,4 glucan phosphorylase

A: Alpha-1,4 glucan phosphorylase


Theoretical massNumber of molelcules
Total (without water)191,1052
Polymers191,1052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein Alpha-1,4 glucan phosphorylase


Mass: 95552.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria)
Gene: malP_2, glgP, glgP_1, glgP_2, ABE91_008520, ACU57_16780, AWP47_17620, BANRA_04427, BCB93_002547, BG944_001231, BK300_15985, BMT50_11700, BMT91_03785, BRV02_001825, BTB68_000085, BvCmsKKP061_ ...Gene: malP_2, glgP, glgP_1, glgP_2, ABE91_008520, ACU57_16780, AWP47_17620, BANRA_04427, BCB93_002547, BG944_001231, BK300_15985, BMT50_11700, BMT91_03785, BRV02_001825, BTB68_000085, BvCmsKKP061_02805, C0P57_004167, C1Q91_001686, C3F40_19100, C719_002287, C9160_12990, C9194_04120, CCS08_20530, CF22_001891, CIG67_16365, CQ842_09205, CQ842_13775, CR538_01800, CTR35_001909, CWS33_11285, DIV22_04120, DL968_00505, DNQ45_04695, DS732_24960, E2863_04678, E5H86_09675, E6D34_04450, ECs4273, EPS97_04380, F9461_03265, FGAF848_24940, FJQ40_03660, FPS11_03160, FV293_09090, G3V95_06220, G4A38_19915, G4A47_18950, GAJ12_07190, GNW61_08685, GOP25_12710, GP944_08480, GP954_08370, GQM04_09305, GQM21_16355, HHH44_000638, HKA49_001161, HLZ50_06375, HMV95_08065, HV109_01555, HV209_14140, HVW43_18125, HVY77_01525, HX136_01560, I6H02_12565, IDONEFKE_02006, IH772_08585, J0541_002177, J5U05_000643, JNA65_09005, JNA68_03435, JNP96_25935, NCTC10279_03905, NCTC10429_00923, NCTC11181_02623, NCTC13148_03616, NCTC8179_05813, NCTC8333_00368, NCTC8500_00162, NCTC8960_02956, NCTC9706_02702, NQD80_14375, NY836_12010, OFN31_07695, P6223_000252, Q2V64_17370, QDW62_01550, SAMEA3752557_02081, TUM18780_03240, WR15_03080
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3SPS5, glycogen phosphorylase
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: glycogen phosphorylase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium chlorideNaCl1
220 mMTris1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 10 mA current / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3 microliters droplet, 20 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging.

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7656

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187286 / Symmetry type: POINT

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