8EKK | pdb_00008ekk

Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 2

PDB DOI: https://doi.org/10.2210/pdb8EKK/pdb
EM Map EMD-28205: EMDB EMDataResource

Classification: TOXIN
Organism(s): Clostridioides difficile R20291
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-09-21 Released: 2023-09-27
Deposition Author(s): Abeyawardhane, D.L., Pozharski, E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 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 8EKK

This is version 1.0 of the entry. See complete history.

Literature

Calcium-mediated Pore Formation of Clostridioides difficile Binary Toxin

Abeyawardhane, D.L., Adipietro, K.A., Ruiz, R.G., Varney, K.M., Rustandi, R.R., Silin, V.I., Pozharski, E., Weber, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 523.31 kDa
Atom Count: 29,624
Modeled Residue Count: 3,731
Deposited Residue Count: 4,669
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyltransferase binding component	A, B, C, D, E A, B, C, D, E, F, G	667	Clostridioides difficile R20291	Mutation(s): 0 Gene Names: cdtB
UniProt
Find proteins for A0A9R0BM17 (Clostridioides difficile (strain R20291)) Explore A0A9R0BM17 Go to UniProtKB: A0A9R0BM17
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0BM17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	H [auth A] I [auth A] J [auth B] K [auth B] L [auth C] H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth D], P [auth E], Q [auth E], R [auth F], S [auth F], T [auth G], U [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth G] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Abeyawardhane, D.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56AI152397

Revision History (Full details and data files)

Version 1.0: 2023-09-27
Type: Initial release

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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.