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- PDB-9wxr: sensory rhodopsin I with its cognate transducer HtrI -

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Basic information

Entry
Database: PDB / ID: 9wxr
Titlesensory rhodopsin I with its cognate transducer HtrI
ComponentsRhodopsin,Chemotaxis protein
KeywordsSIGNALING PROTEIN / sensory rhodopsin / transducer / HAMP domain / phototaxis
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor / 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 (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / Bacterial rhodopsins retinal binding site. / HAMP domain profile. / HAMP domain ...Chemotaxis methyl-accepting receptor / 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 (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / Bacterial rhodopsins retinal binding site. / HAMP domain profile. / HAMP domain / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
RETINAL / Chemotaxis protein / Rhodopsin
Similarity search - Component
Biological speciesHaloarcula taiwanensis (Halophile)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsLim, G.Z. / Lin, Y.E. / Wu, Y.M. / Chen, P.C. / Fu, H.Y. / Yang, C.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of the SRI-HtrI complex reveals the cytoplasmic coupling in an archaeal phototaxis system.
Authors: Guo Zhen Lim / Yu-En Lin / Pei-Chun Chen / Hsu-Yuan Fu / Chii-Shen Yang /
Abstract: Sensory rhodopsins (SRs) in haloarchaea form complexes with their cognate transducers (Htrs) to produce wavelength-specific phototactic responses, yet similar architectures mediate distinct behaviors: ...Sensory rhodopsins (SRs) in haloarchaea form complexes with their cognate transducers (Htrs) to produce wavelength-specific phototactic responses, yet similar architectures mediate distinct behaviors: SRI mediates attraction, SRII drives repulsion, whereas SRM modulates both responses. Until now, structural insight was limited to the Natronomonas pharaonis SRII-HtrII system in a truncated form, without a full-length counterpart for comparison. Moreover, NpHtrII is distinct among HtrII transducers in lacking the large periplasmic domain retained in homologs from Halobacterium salinarum, Haloarcula marismortui and Haloarcula taiwanensis, leaving the canonical SR-Htr architecture unknown. Here, we report the cryo-EM structure of the Haloarcula taiwanensis SRI-HtrI complex, providing a near native, non-crystallized view of a full-length SR-Htr dimer with the cytoplasmic HAMP1 domain resolved. The structure reveals the intact homodimeric receptor-transducer assembly and visualizes the interface between the helix G (Arg215), SRI E-F loop (Pro154), and HtrI HAMP1. These findings fill the long-standing structural gap for a canonical SR-Htr complex and establish a framework for conserved receptor-transducer coupling across archaeal phototaxis systems.
History
DepositionSep 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin,Chemotaxis protein
B: Rhodopsin,Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0944
Polymers77,5252
Non-polymers5692
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Rhodopsin,Chemotaxis protein


Mass: 38762.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HtSRI-linker(ASASNGASAH)-HtrI fusion / Source: (gene. exp.) Haloarcula taiwanensis (Halophile) / Gene: BVU17_02570, BVU17_02575 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A2H4ZVH1, UniProt: A0A2H4ZVF9
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Dimerized complex of HtSRI-HtrI fused with a linker peptide
Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Haloarcula taiwanensis (Halophile)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C43
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
250 mM2-(N-morpholino)ethanesulfonic acidC6H13NO4S1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 190000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 1400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6.0particle selection
2EPUimage acquisition
4cryoSPARC4.6.0CTF correctionAb-initio reconstruction
7UCSF ChimeraX1.10.1model fitting
9PHENIX1.21.2model refinementphenix.real_space_refine
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43979 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 4.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035260
ELECTRON MICROSCOPYf_angle_d0.6477178
ELECTRON MICROSCOPYf_dihedral_angle_d6.156764
ELECTRON MICROSCOPYf_chiral_restr0.042878
ELECTRON MICROSCOPYf_plane_restr0.004894

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