8Z21 | pdb_00008z21

Cryo-EM structure of Escherichia coli OppBCDF in the resting state

• PDB DOI: https://doi.org/10.2210/pdb8Z21/pdb
• EM Map EMD-39742: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-04-12 Released: 2025-04-16 
• Deposition Author(s): Li, P., Huang, Y.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Escherichia coli OppBCDF in the resting state

Li, P., Huang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 141.47 kDa 
• Atom Count: 9,545 
• Modeled Residue Count: 1,235 
• Deposited Residue Count: 1,277 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide transport system permease protein OppB	A	306	Escherichia coli K-12	Mutation(s): 0  Gene Names: oppB, b1244, JW1236 Membrane Entity: Yes
UniProt
Find proteins for P0AFH2 (Escherichia coli (strain K12)) Explore P0AFH2  Go to UniProtKB:  P0AFH2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide transport system permease protein OppC	B	302	Escherichia coli K-12	Mutation(s): 0  Gene Names: oppC, b1245, JW1237 Membrane Entity: Yes
UniProt
Find proteins for P0AFH6 (Escherichia coli (strain K12)) Explore P0AFH6  Go to UniProtKB:  P0AFH6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide transport ATP-binding protein OppD	C	336	Escherichia coli K-12	Mutation(s): 0  Gene Names: oppD, b1246, JW1238 EC: 7.4.2.6 Membrane Entity: Yes
UniProt
Find proteins for P76027 (Escherichia coli (strain K12)) Explore P76027  Go to UniProtKB:  P76027

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide transport ATP-binding protein OppF	D	333	Escherichia coli K-12	Mutation(s): 0  Gene Names: oppF, b1247, JW1239 EC: 7.4.2.6 Membrane Entity: Yes
UniProt
Find proteins for P77737 (Escherichia coli (strain K12)) Explore P77737  Go to UniProtKB:  P77737

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	E [auth C], F [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Li, P., Huang, Y.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release