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 OPM PDBTM

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YL9

This is version 1.1 of the entry. See complete history.

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

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

Find similar proteins by:

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] 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09545
Sequence Annotations Expand
Reference Sequence

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-31

Deposition Author(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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.