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- EMDB-58291: Oxidized E.coli aerotaxis receptor in MH-cap free state -

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Basic information

Entry
Database: EMDB / ID: EMD-58291
TitleOxidized E.coli aerotaxis receptor in MH-cap free state
Map data
Sample
  • Complex: LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state
    • Protein or peptide: Aerotaxis receptor
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsChemotaxis / Energy Taxis / Redox Sensing / Transmembrane Signaling / Cryo-EM / DdEER Spectroscopy / Flavoprotein
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
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsOlsthoorn FA / Muok AR / Xu Y / Crane BR
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58291.png

Downloads & links

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Map

FileDownload / File: emd_58291.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0695
Minimum - Maximum-0.08146092 - 0.17994395
Average (Standard dev.)0.00003362919 (±0.0052246586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58291_msk_1.map
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Half map: #1

Fileemd_58291_half_map_1.map
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Histogram

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Half map: #2

Fileemd_58291_half_map_2.map
Projections & Slices
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Sample components

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Entire : LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state

EntireName: LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state
Components
  • Complex: LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state
    • Protein or peptide: Aerotaxis receptor
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state

SupramoleculeName: LMNG-solubilized Aer bound to cofactor FAD in a Q MH-cap free state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Aerotaxis receptor

MacromoleculeName: Aerotaxis receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 58.002648 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: WSHPQFEKGG GSGGGSGGSA WSHPQFEKMS SHPYVTQQNT PLADDTTLMS TTDLQSYITH ANDTFVQVSG YTLQELQGQP HNMVRHPDM PKAAFADMWF TLKKGEPWSG IVKNRRKNGD HYWVRANAVP MVREGKISGY MSIRTRATDE EIAAVEPLYK A LNAGRTSK ...String:
WSHPQFEKGG GSGGGSGGSA WSHPQFEKMS SHPYVTQQNT PLADDTTLMS TTDLQSYITH ANDTFVQVSG YTLQELQGQP HNMVRHPDM PKAAFADMWF TLKKGEPWSG IVKNRRKNGD HYWVRANAVP MVREGKISGY MSIRTRATDE EIAAVEPLYK A LNAGRTSK RIHKGLVVRK GWLGKLPSLP LRWRARGVMT LMFILLAAML WFVAAPVVTY ILCALVVLLA SACFEWQIVR PI ENVAHQA LKVATGERNS VEHLNRSDEL GLTLRAVGQL GLMCRWLIND VSSQVSSVRN GSETLAKGTD ELNEHTQQTV DNV QQTVAT MNQMAASVKQ NSATASAADK LSITASNAAV QGGEAMTTVI KTMDDIADST QRIGTITSLI NDIAFQTNIL ALNA AVEAA RAGEQGKGFA VVAGEVRHLA SRSANAANDI RKLIDASADK VQSGSQQVHA AGRTMEDIVA QVKNVTQLIA QISHS TLEQ ADGLSSLTRA VDELNLITQK NAELVEESAQ VSAMVKHRAS RLEDAVTVLH

UniProtKB: Aerotaxis receptor

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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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

BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMSodium chlorideNaCl
5.0 %Glycerol
0.002 %LMNG

Details: 25 mM Tris, 150 mM NaCl, 5% glycerol, 0.002% LMNG
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 90018
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Details: Final 2D classification revealed two conformational states: MH-cap bound and MH-cap free. MH-cap bound particles were 2D selected and then subtracted from the MH-cap free particle list.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: ISOLDE
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 147.2
Output model

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

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