9MA8 | pdb_00009ma8

Glycogen phosphorylase from Segatella copri bound to glycogen-chain A and E

• PDB DOI: https://doi.org/10.2210/pdb9MA8/pdb
• EM Map EMD-63749: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Segatella copri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-14 Released: 2026-02-18 
• Deposition Author(s): Shobu, K., Fukuda, Y., Inoue, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and mechanistic diversity of glycogen phosphorylase from gut bacteria

Shobu, K., Takai, M., Fukuda, Y., Inoue, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 199.28 kDa 
• Atom Count: 14,025 
• Modeled Residue Count: 1,704 
• Deposited Residue Count: 1,704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucan family phosphorylase	A, B [auth E]	852	Segatella copri	Mutation(s): 0  Gene Names: glgP, DW064_01070, LYY06_13165
UniProt
Find proteins for A0AA93BMC9 (Segatella copri) Explore A0AA93BMC9  Go to UniProtKB:  A0AA93BMC9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C [auth B]	3		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D [auth C]	5		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G1P (Subject of Investigation/LOI)	E [auth A]	1-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P HXXFSFRBOHSIMQ-VFUOTHLCSA-N
PO4 (Subject of Investigation/LOI)	F [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B [auth E]	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	C [auth B]	alpha-maltotriose	Oligosaccharide / Nutrient

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900030	D [auth C]	alpha-maltopentaose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Shobu, K., Fukuda, Y., Inoue, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release