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- PDB-9s7v: Structure of glycogen phosphorylase - dimeric form - from Escheri... -

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Basic information

Entry
Database: PDB / ID: 9s7v
TitleStructure of glycogen phosphorylase - dimeric form - from Escherichia coli
ComponentsGlycogen phosphorylase
KeywordsTRANSFERASE / Glycogen phosphorylase
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
Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDi Domenico, V. / Mastrella, L. / Alcaide-Jimenez, A. / Villegas-Ruiz, J.C. / D'Angelo, C. / Cifuente, J.O. / Connell, S.R. / Guerin, M.E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: To Be Published
Title: Structural basis for phosphorylation and allosteric regulation of bacterial glycogen phosphorylase by histidine phosphocarrier protein
Authors: Di Domenico, V. / Franceus, J. / Mastrella, L. / De Beul, E. / Alcaide-Jimenez, A. / Villegas-Ruiz, J.C. / Holden, E. / D'Angelo, C. / Cifuente, J.O. / Connell, S.R. / Struwe, W.B. / ...Authors: Di Domenico, V. / Franceus, J. / Mastrella, L. / De Beul, E. / Alcaide-Jimenez, A. / Villegas-Ruiz, J.C. / Holden, E. / D'Angelo, C. / Cifuente, J.O. / Connell, S.R. / Struwe, W.B. / Benesch, J.L.P.B. / Colleoni, C. / Desmet, T. / Guerin, M.E.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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: Glycogen phosphorylase
B: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)191,0732
Polymers191,0732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glycogen phosphorylase


Mass: 95536.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glgP, glgY, b3428, JW3391 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC86, 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: Recombinantly purified Glycogen phosphorylase from E. coli
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.93 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
12EPU3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260408 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312099
ELECTRON MICROSCOPYf_angle_d0.43216543
ELECTRON MICROSCOPYf_dihedral_angle_d10.3434048
ELECTRON MICROSCOPYf_chiral_restr0.0371911
ELECTRON MICROSCOPYf_plane_restr0.0032133

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