9LR7 | pdb_00009lr7

Crystal Structure of the Basal pilin EbpB from Enterococcus faecalis.

PDB DOI: https://doi.org/10.2210/pdb9LR7/pdb

Classification: CELL ADHESION
Organism(s): Enterococcus faecalis OG1RF
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-30 Released: 2025-07-16
Deposition Author(s): Sharma, V., Krishnan, V.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.255 (Depositor), 0.254 (DCC)
R-Value Work:
0.219 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of Ebp pilus shaft formation and anchoring in vancomycin-resistant Enterococci.

Sharma, V., Krishnan, V.

(2025) FEBS J

PubMed: 40608565 Search on PubMed
DOI: https://doi.org/10.1111/febs.70173
Primary Citation of Related Structures:
9LJ6, 9LKS, 9LLW, 9LR7, 9LTY, 9M00

PubMed Abstract:
Enterococcus faecalis is an opportunistic pathogen that causes various clinically significant infections, including infective endocarditis and catheter-associated urinary tract infections. E. faecalis assembles hair-like appendages termed endocarditis and biofilm-associated pili (Ebp), crucial for adherence, colonization, biofilm formation, and virulence. The Ebp pilus comprises three pilin subunits (EbpA, EbpB, and EbpC) encoded by the ebpABC pilus operon. EbpC forms the Ebp pilus backbone decorated with EbpA and EbpB at the tip and base for adhesion and anchoring, respectively. Experimental structures are not yet available for any of the Ebp pilins. Herein, we report the crystal structures of EbpC, EbpB, and their homologs from E. faecium. The structures of EbpC and EbpB reveal four and three linearly arranged immunoglobulin-like domains, respectively. The basal pilin EbpB structure fully mimics the features of backbone pilins with a typical pilin motif and CnaB-CnaA-CnaB fold, each with an intact isopeptide bond. The rigid C-terminal fragment of the backbone pilin EbpC, containing three domains, exhibits a CnaB-CnaA-CnaB fold, each with an intradomain isopeptide bond. The flexible N-terminal domain with the CnaB fold in EbpC lacks an isopeptide bond but appears to form in a full-length structure that shows a 'beads on a string' architecture, previously unobserved for four-domain backbone pilins. Structural analysis helped us to identify residues of internal isopeptide bonds and pilin motifs harboring lysine residues responsible for intermolecular covalent links during sortase-mediated pilus assembly and propose a structural model for the Ebp pilus. This knowledge may be useful for developing structure-based approaches targeting pilins and pili in enterococcal infections.

Organizational Affiliation

Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.

Macromolecule Content

Total Structure Weight: 195.65 kDa
Atom Count: 11,888
Modeled Residue Count: 1,540
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endocarditis and biofilm-associated pilus minor subunit EbpB	A [auth B], B [auth A], C, D	436	Enterococcus faecalis OG1RF	Mutation(s): 0 Gene Names: ebpB, GTI81_12235
UniProt
Find proteins for A0AAP6RJI4 (Enterococcus faecalis) Explore A0AAP6RJI4 Go to UniProtKB: A0AAP6RJI4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAP6RJI4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth A] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth B] MOL2 format, chain O [auth A] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth B] mmCIF format, chain O [auth A] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	H [auth B], O [auth A], T [auth C], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Focus chain O [auth A] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain H [auth B] Focus chain O [auth A] Focus chain T [auth C] Focus chain Y [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth A] SDF format, chain Z [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth D]	J [auth B], P [auth A], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth A] Focus chain Z [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth A] Focus chain Z [auth D]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain F [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain F [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] mmCIF format, chain F [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	E [auth B] F [auth B] G [auth B] I [auth B] K [auth A] E [auth B], F [auth B], G [auth B], I [auth B], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth C], R [auth C], S [auth C], U [auth C], V [auth D], W [auth D], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]