8YPT

Cryo-EM structure of BfUbb-ButCD complex

• PDB DOI: https://doi.org/10.2210/pdb8YPT/pdb
• EM Map EMD-39493: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-03-18 Released: 2024-09-25 
• Deposition Author(s): Xu, J.H., Chen, Z., Gao, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues

Xu, J.H., Chen, Z., Gao, X.

(2024) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 327.14 kDa 
• Atom Count: 23,068 
• Modelled Residue Count: 2,894 
• Deposited Residue Count: 2,894 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein	A, B	423	Bacteroides fragilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2M9UVJ9 (Bacteroides fragilis) Explore A0A2M9UVJ9  Go to UniProtKB:  A0A2M9UVJ9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TonB-linked outer membrane protein	C, D	986	Bacteroides fragilis	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein	E	76	Bacteroides fragilis	Mutation(s): 0  Gene Names: O1404_18505

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Xu, J.H., Chen, Z., Gao, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release