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- PDB-31ck: Oxidized E.coli aerotaxis receptor in MH-cap free state -

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Basic information

Entry
Database: PDB / ID: 31ck
TitleOxidized E.coli aerotaxis receptor in MH-cap free state
ComponentsAerotaxis receptor
KeywordsFLAVOPROTEIN / Chemotaxis / Energy Taxis / Redox Sensing / Transmembrane Signaling / Cryo-EM / DdEER Spectroscopy
Function / homology
Function and homology information


positive aerotaxis / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
: / Chemotaxis methyl-accepting receptor / PAS fold-3 / PAS fold / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP domain ...: / Chemotaxis methyl-accepting receptor / PAS fold-3 / PAS fold / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Aerotaxis receptor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsOlsthoorn, F.A. / Muok, A.R. / Xu, Y. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GMR35122535 United States
CitationJournal: bioRxiv / Year: 2026
Title: Signaling mechanism of the transmembrane energy receptor Aer.
Authors: Flory A Olsthoorn / Alise R Muok / Zachary A Maschmann / Yajie Xu / Siddarth Chandrasekaran / Robert Dunleavy / Brian R Crane
Abstract: The aerotaxis receptor Aer is a bacterial chemoreceptor that senses intracellular redox changes via an N-terminal PAS domain bound to a flavin adenine dinucleotide (FAD) cofactor. Distinct from ...The aerotaxis receptor Aer is a bacterial chemoreceptor that senses intracellular redox changes via an N-terminal PAS domain bound to a flavin adenine dinucleotide (FAD) cofactor. Distinct from canonical methyl-accepting chemotaxis proteins (MCPs) such as Tar/Tsr, Aer lacks a periplasmic ligand-binding domain and adaptive methylation, transmitting conformational signals laterally from the PAS domain to the HAMP domain and the methylation helix cap (MH-cap) of the kinase control domain (KCD). To elucidate the Aer signalling mechanism, we determined cryo-electron microscopy (cryo-EM) structures of full-length Aer in oxidized flavin quinone (kinase-on) and anionic semiquinone (kinase-off) states. Structural comparison revealed redox-linked rearrangements of the FAD-binding pocket, reorientation of PAS-HAMP interactions, and strikingly altered MH-cap stability. PAS-MH-cap contact in the oxidized state compressed the receptor and stabilized proximal KCD helices, whereas reduction disrupted these contacts, increasing KCD flexibility. To probe distal effects on KCD architecture, we performed nanodisc reconstitution and pulse dipolar ESR spectroscopy on spin-labelled positions along the four-helix bundle. Distance distributions indicated redox-dependent changes in helix separation, particularly at the C-terminal MH2 region, consistent with PAS-driven loosening of KCD packing in kinase-off states. These data support a model in which FAD redox chemistry reorganizes flavin pocket residues that in turn subtly alter PAS conformation to influence PAS-HAMP and PAS-MH-cap packing and hence KCD conformational stability. The findings reveal an Aer-specific signaling axis distinct from periplasmic-ligand binding MCPs that has adapted MCP architecture for lateral PAS input and and cytoplasmic redox sensing.
History
DepositionMay 25, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerotaxis receptor
B: Aerotaxis receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5764
Polymers116,0052
Non-polymers1,5712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Aerotaxis receptor


Mass: 58002.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: aer, air, yqjJ, b3072, JW3043 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50466
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET28
Buffer solutionpH: 7.5 / Details: 25 mM Tris, 150 mM NaCl, 5% glycerol, 0.002% LMNG
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris1
2150 mMSodium chlorideNaCl1
35 %Glycerol1
40.002 %LMNG1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
5cryoSPARCCTF correction
8ISOLDEmodel fitting
9UCSF ChimeraXmodel fitting
10Cootmodel fitting
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
16PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90018 / Symmetry type: POINT
Atomic model buildingB value: 147.2 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034116
ELECTRON MICROSCOPYf_angle_d0.625610
ELECTRON MICROSCOPYf_dihedral_angle_d8636
ELECTRON MICROSCOPYf_chiral_restr0.042632
ELECTRON MICROSCOPYf_plane_restr0.004688

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