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- PDB-9u3a: Glycogen phosphorylase from Segatella copri in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 9u3a
TitleGlycogen phosphorylase from Segatella copri in complex with AMP
ComponentsAlpha-glucan family phosphorylase
KeywordsSTRUCTURAL PROTEIN / glycogen metabolism / cryo-EM / gut bacteria
Function / homology
Function and homology information


glycogen phosphorylase activity / pyridoxal phosphate binding / carbohydrate metabolic process
Similarity search - Function
Alpha-glucan phosphorylase / Glycogen phosphorylase, domain of unknown function DUF3417 / : / Protein of unknown function (DUF3417) / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Alpha-glucan family phosphorylase
Similarity search - Component
Biological speciesSegatella copri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsShobu, K. / 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 phosphorylase from gut bacteria
Authors: Shobu, K. / Takai, M. / Fukuda, Y. / Inoue, T.
History
DepositionMar 18, 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-glucan family phosphorylase
B: Alpha-glucan family phosphorylase
C: Alpha-glucan family phosphorylase
D: Alpha-glucan family phosphorylase
E: Alpha-glucan family phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,75713
Polymers493,9805
Non-polymers2,7788
Water00
1


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

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Components

#1: Protein
Alpha-glucan family phosphorylase


Mass: 98795.938 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence refers to WP_218459193.1 in NCBI / Source: (gene. exp.) Segatella copri (bacteria) / Gene: glgP, DW064_01070, LYY06_13165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA93BMC9
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
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: #1 / Source: RECOMBINANT
Source (natural)Organism: Segatella copri (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
220 mMTris1
35 mMadenosine monophosphateAMP1
SpecimenConc.: 4.58 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: 281 K
Details: 3 microliters droplet, 5 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: 6271

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188698 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00435864
ELECTRON MICROSCOPYf_angle_d0.64848585
ELECTRON MICROSCOPYf_dihedral_angle_d9.7874851
ELECTRON MICROSCOPYf_chiral_restr0.0435022
ELECTRON MICROSCOPYf_plane_restr0.0046251

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