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- EMDB-53315: EM structure of Rec-controlled histidine kinase LvrB, BeF3-activated -

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Basic information

Entry
Database: EMDB / ID: EMD-53315
TitleEM structure of Rec-controlled histidine kinase LvrB, BeF3-activated
Map data
Sample
  • Complex: Activated LvrB homodimer
    • Protein or peptide: histidine kinase
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water
KeywordsHistidine Kinase / SIGNALING PROTEIN
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / signal transduction / ATP binding / metal ion binding
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
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.92 Å
AuthorsAgustoni E / Mechaly A / Rizza JD / Beriashvili D / Pluhackova K / Isaikina P / Trajtenberg F / Muntener T / Wunder E / Ko A ...Agustoni E / Mechaly A / Rizza JD / Beriashvili D / Pluhackova K / Isaikina P / Trajtenberg F / Muntener T / Wunder E / Ko A / Schirmer T / Buschiazzo A / Hiller S
Funding support Switzerland, Germany, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation180541 Switzerland
Germanys Excellence Strategy390740016 Germany
CitationJournal: To Be Published
Title: Leptospira virulence factor LvrB unveils the activation mechanism of Rec-controlled histidine kinases
Authors: Agustoni E / Mechaly A / Rizza JD / Beriashvili D / Pluhackova K / Isaikina P / Trajtenberg F / Muntener T / Wunder E / Ko A / Schirmer T / Buschiazzo A / Hiller S
History
DepositionApr 2, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53315.png

Downloads & links

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Map

FileDownload / File: emd_53315.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 224.768 Å		0.88 Å/pix.
x 256 pix.
= 224.768 Å		0.88 Å/pix.
x 256 pix.
= 224.768 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.032313388 - 0.07854076
Average (Standard dev.)0.00012878947 (±0.0034437096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 224.768 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53315_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53315_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Activated LvrB homodimer

EntireName: Activated LvrB homodimer
Components
  • Complex: Activated LvrB homodimer
    • Protein or peptide: histidine kinase
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Activated LvrB homodimer

SupramoleculeName: Activated LvrB homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)

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Macromolecule #1: histidine kinase

MacromoleculeName: histidine kinase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Molecular weightTheoretical: 43.426566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKWKFLFLE DSLVDLELIQ RQLNRAKIDY YPIHVSDSEG FSQAILDQKP HLILSDFSLP KYDGFSALKL AKKICPTTPF IFVSGTYGE EAAIQTLTMG ATDYVLKDRI EKLLPAVQRA LHELEDHELR IKAEKERYEL EEQLRQSQKL EAMGVMAGTM A HEINNPLI ...String:
MNKWKFLFLE DSLVDLELIQ RQLNRAKIDY YPIHVSDSEG FSQAILDQKP HLILSDFSLP KYDGFSALKL AKKICPTTPF IFVSGTYGE EAAIQTLTMG ATDYVLKDRI EKLLPAVQRA LHELEDHELR IKAEKERYEL EEQLRQSQKL EAMGVMAGTM A HEINNPLI AISEYAAMIA KGEVDSEKAK QLASKIRDES ARISTIMKNL LRFSRDDKGS LYPVEVGEIL VKLESITQQI FK MNRIDAS WKNVEPGHSI QCREGQILQI LLNLVNNAVD SLNQKYPEYD TEKRIILENS IVEENHKKYA EFSIQDFGTG IPI DIQKSI FKTFFTTKSA DKGTGLGLSV SLGIAKEHGG SLNFESEPGR YTRFYLRVPI FDPSVQ

UniProtKB: histidine kinase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
5.0 mMMgCl2Magnesium dichloride
30.0 mMC8H18N2O4SHepes

Details: 200 mM NaCl. 30 mM Hepes, 5 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.48 sec. / Average electron dose: 59.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Particle selectionNumber selected: 9270584
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model / Details: Ab initio model generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129432
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Details: NU-refinement cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Details: NU-refinement cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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