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 9QIH | pdb_00009qih

Structure of response regulator LvrC from Leptospira


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.253 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira.

Agustoni, E., Mechaly, A., Dalla Rizza, J., Beriashvili, D., Pluhackova, K., Isaikina, P., Trajtenberg, F., Muntener, T., Wunder Jr., E.A., Ko, A.I., Schirmer, T., Buschiazzo, A., Hiller, S.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-71783-4
  • Primary Citation Related Structures: 
    8VC9, 9QIH, 9QJG, 9QL9, 9QQW, 9QR2

  • PubMed Abstract: 

    Pathogenic Leptospira modulate their virulence via the Lvr signaling system, with the histidine kinase LvrB being a central element. LvrB is a prototype of Rec-controlled histidine kinases, which are frequently found in bacterial two-component systems, and yet whose regulatory mechanisms remain largely unknown. Here, we report full-length structures of LvrB in different states uncovering its mechanism of activation. Kinase-inactive LvrB is a symmetric homodimer, with its catalytic domains rigidly clasped onto the central helical domain. Phosphorylation of the N-terminal Rec domains induces coiled-coil formation of the central αS helices thereby breaking symmetry through liberation of the catalytic domains into a dynamic, auto-phosphorylation competent state. We further identified LvrB's downstream effector partner LvrC, an anti-σ factor that reprograms the transcription of hundreds of virulence genes. Our findings set a mechanistic paradigm for Rec-controlled histidine kinases enabling the design of virulence inhibitors.


  • Organizational Affiliation: 
    • Biozentrum, University of Basel, Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 69.77 kDa 
  • Atom Count: 4,929 
  • Modeled Residue Count: 590 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SenB
A, B
304Leptospira interrogansMutation(s): 0 
Gene Names: senB
UniProt
Find proteins for Q9APH2 (Leptospira interrogans)
Explore Q9APH2 
Go to UniProtKB:  Q9APH2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9APH2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.253 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.289α = 90
b = 85.21β = 90
c = 111.271γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novartis FreeNovationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-10-07
    Changes: Database references