8YAQ | pdb_00008yaq

Cryo-EM structure of cellodextrin phosphorylase from Clostridium thermocellum with cellodextrin ligands

• PDB DOI: https://doi.org/10.2210/pdb8YAQ/pdb
• EM Map EMD-39104: EMDB EMDataResource

• Classification: CARBOHYDRATE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-09 Released: 2025-02-12 
• Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Enzyme-Directed Assembly of Antiparallel Cellulose II Nanocrystals: Unraveling the Mechanism Beyond Spontaneous Crystallization.

Kuga, T., Sunagawa, N., Kobayashi, K., Yamada, H., Imai, T., Uchihashi, T., Igarashi, K.

(2026) JACS Au 6: 154-165

• PubMed: 41614162 
• DOI: https://doi.org/10.1021/jacsau.5c00993
• Primary Citation Related Structures: 
  8YAQ


• PubMed Abstract: 
  

  Humans have long utilized cellulose II, known as regenerated cellulose, for fibers like rayon and Cupra and films like cellophane. While cellulose I, found in nature, consists of parallel molecular chains, cellulose II is characterized by the stable arrangement of molecules in an antiparallel orientation. Enzymatic synthesis of cellulose in vitro also affords cellulose II with various morphologies, from monolayer lamellae crystals to gels, but its formation mechanism remains obscure. Here, we demonstrate that cellodextrin phosphorylase (CDP) catalyzes the synthesis and orchestrates the antiparallel self-assembly of cellulose II nanocrystals, exceeding the paradigm of spontaneous crystallization. High-resolution structural analysis reveals CDP's key role in dictating crystal size and alignment, bridging the gap between enzymatic catalysis and biodirected material architecture. Our research unveils a unique protein-templated assembly process for advanced cellulose materials, paving the way for enzyme-guided construction of next-generation functional nanostructures.

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Organizational Affiliation: 
• Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
Department of Physics and Structural Biology Research Centre, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0814, Japan.
VTT Technical Research Centre of Finland, Tietotie 2 VTT, P.O. Box 1000, 02044 Espoo, Finland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 226.71 kDa 
• Atom Count: 15,860 
• Modeled Residue Count: 1,969 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellodextrin phosphorylase	A, B	990	Acetivibrio thermocellus	Mutation(s): 0  Gene Names: cdp-ym4
UniProt
Find proteins for Q93HT8 (Acetivibrio thermocellus) Explore Q93HT8  Go to UniProtKB:  Q93HT8

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C [auth D]	5		N/A
Glycosylation Resources
GlyTouCan: G91683DU GlyCosmos: G91683DU

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D [auth C]	3		N/A
Glycosylation Resources
GlyTouCan: G14338VK GlyCosmos: G14338VK GlyGen: G14338VK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	C [auth D]	beta-cellopentaose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021	D [auth C]	beta-cellotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.0
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12566
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H05494

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Data collection, Database references