8BIY | pdb_00008biy

Citrate-free extracytoplasmic PAS domain mutant R93A of sensor histidine kinase CitA from Geobacillus thermodenitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Mechanism of sensor kinase CitA transmembrane signaling.

Zhang, X.C.Xue, K.Salvi, M.Schomburg, B.Mehrens, J.Giller, K.Stopp, M.Weisenburger, S.Boning, D.Sandoghdar, V.Unden, G.Becker, S.Andreas, L.B.Griesinger, C.

(2025) Nat Commun 16: 935-935

  • DOI: https://doi.org/10.1038/s41467-024-55671-3
  • Primary Citation Related Structures: 
    8BGB, 8BIY, 8BJP

  • PubMed Abstract: 

    Membrane bound histidine kinases (HKs) are ubiquitous sensors of extracellular stimuli in bacteria. However, a uniform structural model is still missing for their transmembrane signaling mechanism. Here, we used solid-state NMR in conjunction with crystallography, solution NMR and distance measurements to investigate the transmembrane signaling mechanism of a paradigmatic citrate sensing membrane embedded HK, CitA. Citrate binding in the sensory extracytoplasmic PAS domain (PASp) causes the linker to transmembrane helix 2 (TM2) to adopt a helical conformation. This triggers a piston-like pulling of TM2 and a quaternary structure rearrangement in the cytosolic PAS domain (PASc). Crystal structures of PASc reveal both anti-parallel and parallel dimer conformations. An anti-parallel to parallel transition upon citrate binding agrees with interdimer distances measured in the lipid embedded protein using a site-specific 19 F label in PASc. These data show how Angstrom scale structural changes in the sensor domain are transmitted across the membrane to be converted and amplified into a nm scale shift in the linker to the phosphorylation subdomain of the kinase.


  • Organizational Affiliation
    • NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 57.52 kDa 
  • Atom Count: 4,324 
  • Modeled Residue Count: 502 
  • Deposited Residue Count: 524 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histidine kinase
A, B, C, D
131Geobacillus thermodenitrificansMutation(s): 2 
Gene Names: dctS_2GTHT12_01458
EC: 2.7.13.3

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CXS

Query on CXS



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth C],
L [auth D]
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth B],
J [auth C],
M [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.137α = 90
b = 120.053β = 90
c = 152.137γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XPREPdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-11-15 
  • Deposition Author(s): Becker, S.

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references, Structure summary
  • Version 1.2: 2026-03-04
    Changes: Refinement description