8Z1Z | pdb_00008z1z

Cryo-EM structure of Escherichia coli DppAR383D+D436RBCDF in pre-catalytic state

• PDB DOI: https://doi.org/10.2210/pdb8Z1Z/pdb
• EM Map EMD-39741: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Escherichia coli DppAR383DD436RBCDF in the catalytic intermediate state

Li, P., Huang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 205.47 kDa 
• Atom Count: 13,652 
• Modeled Residue Count: 1,740 
• Deposited Residue Count: 1,835 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptide transport system permease protein DppB	A	339	Escherichia coli K-12	Mutation(s): 0  Gene Names: dppB, b3543, JW3512
UniProt
Find proteins for P0AEF8 (Escherichia coli (strain K12)) Explore P0AEF8  Go to UniProtKB:  P0AEF8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptide transport system permease protein DppC	B	300	Escherichia coli K-12	Mutation(s): 0  Gene Names: dppC, b3542, JW3511
UniProt
Find proteins for P0AEG1 (Escherichia coli (strain K12)) Explore P0AEG1  Go to UniProtKB:  P0AEG1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptide transport ATP-binding protein DppD	C	327	Escherichia coli K-12	Mutation(s): 0  Gene Names: dppD, b3541, JW3510 EC: 7.4.2.9
UniProt
Find proteins for P0AAG0 (Escherichia coli (strain K12)) Explore P0AAG0  Go to UniProtKB:  P0AAG0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptide transport ATP-binding protein DppF	D	334	Escherichia coli K-12	Mutation(s): 0  Gene Names: dppF, dppE, b3540, JW3509 EC: 7.4.2.9
UniProt
Find proteins for P37313 (Escherichia coli (strain K12)) Explore P37313  Go to UniProtKB:  P37313

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptide-binding protein	E [auth F]	535	Escherichia coli K-12	Mutation(s): 2  Gene Names: dppA, b3544, JW3513
UniProt
Find proteins for P23847 (Escherichia coli (strain K12)) Explore P23847  Go to UniProtKB:  P23847

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS (Subject of Investigation/LOI)	G [auth C], I [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)	F [auth C], H [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 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