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- PDB-9qjg: CA domain of LvrB from Leptospira with bound ADP -

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Basic information

Entry
Database: PDB / ID: 9qjg
TitleCA domain of LvrB from Leptospira with bound ADP
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / Leptospirosis / histidine kinase / response regulator
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / signal transduction
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / histidine kinase
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHiller, S. / Agustoni, E. / Buschiazzo, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Novartis FreeNovation Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira.
Authors: Elia Agustoni / Ariel Mechaly / Joaquín Dalla Rizza / David Beriashvili / Kristyna Pluhackova / Polina Isaikina / Felipe Trajtenberg / Thomas Müntener / Elsio A Wunder / Albert I Ko / ...Authors: Elia Agustoni / Ariel Mechaly / Joaquín Dalla Rizza / David Beriashvili / Kristyna Pluhackova / Polina Isaikina / Felipe Trajtenberg / Thomas Müntener / Elsio A Wunder / Albert I Ko / Tilman Schirmer / Alejandro Buschiazzo / Sebastian Hiller /
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 ...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.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1814
Polymers39,3262
Non-polymers8542
Water5,152286
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-22 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.132, 54.899, 135.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein histidine kinase


Mass: 19663.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: LA_2223 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8F424, histidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris, 100 mM MgCl2, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000039 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000039 Å / Relative weight: 1
ReflectionResolution: 1.6→42.71 Å / Num. obs: 50363 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 14.91 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Rrim(I) all: 0.096 / Net I/σ(I): 26.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 6.73 / Num. unique obs: 4979 / CC1/2: 0.959 / CC star: 0.99 / Rpim(I) all: 0.22 / Rrim(I) all: 0.81 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.71 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2272 2579 5.12 %
Rwork0.2044 --
obs0.2056 50363 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 54 286 2830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062596
X-RAY DIFFRACTIONf_angle_d1.0793512
X-RAY DIFFRACTIONf_dihedral_angle_d14.485352
X-RAY DIFFRACTIONf_chiral_restr0.068387
X-RAY DIFFRACTIONf_plane_restr0.006443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.30691300.25292632X-RAY DIFFRACTION100
1.63-1.660.28861550.24122630X-RAY DIFFRACTION100
1.66-1.70.24661380.21462594X-RAY DIFFRACTION100
1.7-1.740.22921410.21132623X-RAY DIFFRACTION100
1.74-1.780.22911320.2212629X-RAY DIFFRACTION100
1.78-1.830.21771430.21392624X-RAY DIFFRACTION100
1.83-1.890.2681500.21742603X-RAY DIFFRACTION100
1.89-1.950.26191420.22492633X-RAY DIFFRACTION100
1.95-2.020.22681370.21232636X-RAY DIFFRACTION100
2.02-2.10.20261300.20312639X-RAY DIFFRACTION100
2.1-2.190.22691480.20132665X-RAY DIFFRACTION100
2.19-2.310.22291280.20232635X-RAY DIFFRACTION100
2.31-2.450.23171330.20312652X-RAY DIFFRACTION100
2.45-2.640.22591470.20642686X-RAY DIFFRACTION100
2.64-2.910.23361560.20442638X-RAY DIFFRACTION100
2.91-3.330.23061540.20362699X-RAY DIFFRACTION100
3.33-4.190.21031570.18782728X-RAY DIFFRACTION100
4.19-42.710.20861580.19372838X-RAY DIFFRACTION100

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