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- EMDB-63157: cryo-EM structure of a nanobody bound heliorhodopsin -

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Basic information

Entry
Database: EMDB / ID: EMD-63157
Titlecryo-EM structure of a nanobody bound heliorhodopsin
Map data
Sample
  • Complex: dimer complex
    • Protein or peptide: Heliorhodopsin
    • Protein or peptide: nanobody B4
  • Ligand: RETINAL
  • Ligand: ACETATE ION
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: PALMITIC ACID
Keywordsbacterial rhodopsin / MEMBRANE PROTEIN
Function / homologyHeliorhodopsin / Heliorhodopsin / membrane / Heliorhodopsin
Function and homology information
Biological speciesEscherichia coli (E. coli) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsHe Y / Xia R
Funding support China, 1 items
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, 2025-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63157.png

Downloads & links

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Map

FileDownload / File: emd_63157.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-4.5913424 - 7.1684227
Average (Standard dev.)0.0020425634 (±0.12693381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63157_msk_1.map
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Half map: #2

Fileemd_63157_half_map_1.map
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Half map: #1

Fileemd_63157_half_map_2.map
Projections & Slices
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Sample components

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Entire : dimer complex

EntireName: dimer complex
Components
  • Complex: dimer complex
    • Protein or peptide: Heliorhodopsin
    • Protein or peptide: nanobody B4
  • Ligand: RETINAL
  • Ligand: ACETATE ION
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: PALMITIC ACID

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Supramolecule #1: dimer complex

SupramoleculeName: dimer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Heliorhodopsin

MacromoleculeName: Heliorhodopsin / type: protein_or_peptide / ID: 1
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.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.026078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKPTVKEIK SLQNFNRIAG VFHLLQMLAV LALANDFALP MTGTYLNGPP GTTFSAPVVI LETPVGLAVA LFLGLSALFH FIVSSGNFF KRYSASLMKN QNIFRWVEYS LSSSVMIVLI AQICGIADIV ALLAIFGVNA SMILFGWLQE KYTQPKDGDL L PFWFGCIA ...String:
MAKPTVKEIK SLQNFNRIAG VFHLLQMLAV LALANDFALP MTGTYLNGPP GTTFSAPVVI LETPVGLAVA LFLGLSALFH FIVSSGNFF KRYSASLMKN QNIFRWVEYS LSSSVMIVLI AQICGIADIV ALLAIFGVNA SMILFGWLQE KYTQPKDGDL L PFWFGCIA GIVPWIGLLI YVIAPGSTSD VAVPGFVYGI IISLFLFFNS FALVQYLQYK GKGKWSNYLR GERAYIVLSL VA KSALAWQ IFSGTLIPA

UniProtKB: Heliorhodopsin

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Macromolecule #2: nanobody B4

MacromoleculeName: nanobody B4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.289878 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVQLVESGGG LVQAGGSLRL SCAASGMAFS ISRMEWHRQA PGNERELVAR ITGGGRTTYG DSVKGRFTIS RDNAKSMVYL QMNSLKPED TAVYYCNTGY FWGQGTQVTV SSAAALEHHH HHH

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Macromolecule #3: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 3 / Number of copies: 2 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #4: ACETATE ION

MacromoleculeName: ACETATE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ACT
Molecular weightTheoretical: 59.044 Da
Chemical component information

ChemComp-ACT:
ACETATE ION

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Macromolecule #5: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239778
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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