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- PDB-9ljj: cryo-EM structure of a nanobody bound heliorhodopsin -

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Basic information

Entry
Database: PDB / ID: 9ljj
Titlecryo-EM structure of a nanobody bound heliorhodopsin
Components
  • Heliorhodopsin
  • nanobody B4
KeywordsMEMBRANE PROTEIN / bacterial rhodopsin
Function / homologyHeliorhodopsin / Heliorhodopsin / membrane / ACETATE ION / PALMITIC ACID / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / RETINAL / Heliorhodopsin
Function and homology information
Biological speciesEscherichia coli (E. coli)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsHe, Y. / Xia, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070048 China
CitationJournal: Biochem Biophys Res Commun / Year: 2025
Title: Cryo-EM structure of a nanobody-bound heliorhodopsin.
Authors: Ruixue Xia / Mingxia Sun / Yang Lu / Na Wang / Anqi Zhang / Changyou Guo / Zhenmei Xu / Xuehui Cai / Yuanzheng He /
Abstract: Heliorhodopsins (HeRs) represent a distinct class of microbial rhodopsins (MRs) with an inverted membrane topology compared to other MRs. Previous structural studies have shown that HeRs lack a ...Heliorhodopsins (HeRs) represent a distinct class of microbial rhodopsins (MRs) with an inverted membrane topology compared to other MRs. Previous structural studies have shown that HeRs lack a proton acceptor residue, and protons are never released from the protein. In this study, we present the cryo-electron microscopy (cryo-EM) structure of HeR bound to a nanobody. The structure reveals an acetate-like molecule in the Schiff base cavity (SBC) on the intracellular side of HeR under neutral condition. Structural comparisons and analyses suggest that the acetate molecule may function as a proton acceptor for the protonated retinal Schiff base (RSB) and act as a mediator for the intramolecular signaling transduction in HeR during light stimulation. These structural insights shed new light on the mechanism and function of HeR.
History
DepositionJan 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heliorhodopsin
B: Heliorhodopsin
M: nanobody B4
N: nanobody B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,62412
Polymers82,6324
Non-polymers1,9928
Water00
1


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

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Components

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Protein / Antibody , 2 types, 4 molecules ABMN

#1: Protein Heliorhodopsin


Mass: 28026.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Escherichia coli is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A2R4S913.
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2R4S913
#2: Antibody nanobody B4


Mass: 13289.878 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H52O8P
#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2

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Details

Has ligand of interestN
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: dimer complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239778 / Symmetry type: POINT

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