9QR2 | pdb_00009qr2

EM structure of Rec-controlled histidine kinase LvrB

PDB DOI: https://doi.org/10.2210/pdb9QR2/pdb
EM Map EMD-53316: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-02 Released: 2026-04-15
Deposition Author(s): Agustino, E., Buschiazzo, A., Hiller, S., Beriashvili, D.
Funding Organization(s): Swiss National Science Foundation, Germanys Excellence Strategy

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9QR2

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

Literature

Leptospira virulence factor LvrB unveils the activation mechanism of Rec-controlled histidine kinases

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

To be published.

Macromolecule Content

Total Structure Weight: 87.95 kDa
Atom Count: 6,028
Modeled Residue Count: 752
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine kinase	A, B	382	Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130	Mutation(s): 0 Gene Names: LIC_11708 EC: 2.7.13.3
UniProt
Find proteins for Q72RN7 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)) Explore Q72RN7 Go to UniProtKB: Q72RN7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72RN7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Beriashvili, D.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	180541
Germanys Excellence Strategy	Germany	390740016

Revision History (Full details and data files)

Version 1.0: 2026-04-15
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.