7YL9 | pdb_00007yl9

Cryo-EM structure of complete transmembrane channel E289A mutant Vibrio cholerae Cytolysin

• PDB DOI: https://doi.org/10.2210/pdb7YL9/pdb
• EM Map EMD-33215: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2022-07-25 Released: 2022-08-31 
• Deposition Author(s): Mondal, A.K., Sengupta, N., Singh, M., Biswas, R., Lata, K., Lahiri, I., Dutta, S., Chattopadhyay, K.
• Funding Organization(s): Department of Biotechnology (DBT, India), Department of Science & Technology (DST, India)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of complete transmembrane channel E289A mutant Vibrio cholerae Cytolysin

Mondal, A.K., Sengupta, N., Singh, M., Biswas, R., Lata, K., Lahiri, I., Dutta, S., Chattopadhyay, K.

(null) J Biological Chem 

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 460.02 kDa 
• Atom Count: 31,115 
• Modeled Residue Count: 4,067 
• Deposited Residue Count: 4,151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M], G [auth N]	593	Vibrio cholerae	Mutation(s): 1  Gene Names: hlyA_3, hlyA_2, D6U24_17690, ERS013199_02025, ERS013202_03387 Membrane Entity: Yes
UniProt
Find proteins for P09545 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P09545  Go to UniProtKB:  P09545

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 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: 2022-08-31 
Deposition Author(s): Mondal, A.K., Sengupta, N., Singh, M., Biswas, R., Lata, K., Lahiri, I., Dutta, S., Chattopadhyay, K.

---

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/INF/22/SP22844/2017
Department of Science & Technology (DST, India)	India	SR/FST/LSII-039/2015

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary