9E08 | pdb_00009e08

Cryo-EM structure of MdoD from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb9E08/pdb
• EM Map EMD-47352: EMDB EMDataResource

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-17 Released: 2025-08-27 
• Deposition Author(s): Deme, J.C., Bryant, O.J., Berks, B.C., Lea, S.M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the twin-arginine protein translocation pathway core complex and the molecular basis for substrate recognition

Deme, J.C., Bryant, O.J., Berks, B.C., Lea, S.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 125.83 kDa 
• Atom Count: 8,304 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucans biosynthesis protein D	A, B	552	Escherichia coli	Mutation(s): 0  Gene Names:  opgD, mdoD, BGM66_002243, BJI68_05615, CTR35_003307, E4K51_22440, E6D34_24965, FOI11_006015, FOI11_12985, FWK02_00580, GNW61_13365, GP965_04670, GRW05_15845, HMV95_17475, IH772_11360, J0541_003971, P6223_003218
UniProt
Find proteins for P40120 (Escherichia coli (strain K12)) Explore P40120  Go to UniProtKB:  P40120

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Deme, J.C., Bryant, O.J., Berks, B.C., Lea, S.M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L000776/1
Wellcome Trust	United Kingdom	107929/Z/15/Z
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release