9VBM | pdb_00009vbm

Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (dimer form)

PDB DOI: https://doi.org/10.2210/pdb9VBM/pdb
EM Map EMD-64927: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Dorea longicatena
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-04 Released: 2026-02-18
Deposition Author(s): Takai, M., Tanino, H., Shobu, K., Fukuda, Y., Inoue, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.19 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria

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

To be published.

Macromolecule Content

Total Structure Weight: 88.22 kDa
Atom Count: 6,052
Modeled Residue Count: 751
Deposited Residue Count: 769
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,4 glucan phosphorylase	A	769	Dorea longicatena	Mutation(s): 0 Gene Names: glgP, malP_2, ERS852423_02459, GT528_00800 EC: 2.4.1.1
UniProt
Find proteins for A0A174FL20 (Dorea longicatena) Explore A0A174FL20 Go to UniProtKB: A0A174FL20
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A174FL20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.19 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.0
MODEL REFINEMENT	PHENIX	1.21.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.