8HO8

The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum in complex with cellobiose

PDB DOI: https://doi.org/10.2210/pdb8HO8/pdb
EM Map EMD-34922: EMDB EMDataResource

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

Deposited: 2022-12-09 Released: 2023-12-13
Deposition Author(s): Iriya, S., Kuga, T., Sunagawa, N., Igarashi, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum in complex with cellobiose

Iriya, S., Kuga, T., Sunagawa, N., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 188.43 kDa
Atom Count: 13,454
Modelled Residue Count: 1,618
Deposited Residue Count: 1,634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose phosphorylase	A, B	817	Acetivibrio thermocellus	Mutation(s): 0 Gene Names: cbp EC: 2.4.1.20
UniProt
Find proteins for Q8VP44 (Acetivibrio thermocellus) Explore Q8VP44 Go to UniProtKB: Q8VP44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VP44
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	C, D	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12566

Revision History (Full details and data files)

Version 1.0: 2023-12-13
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.