9LJJ | pdb_00009ljj

cryo-EM structure of a nanobody bound heliorhodopsin

PDB DOI: https://doi.org/10.2210/pdb9LJJ/pdb
EM Map EMD-63157: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli, Vicugna pacos
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2025-01-15 Released: 2025-02-12
Deposition Author(s): He, Y., Xia, R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of a nanobody-bound heliorhodopsin.

Xia, R., Sun, M., Lu, Y., Wang, N., Zhang, A., Guo, C., Xu, Z., Cai, X., He, Y.

(2025) Biochem Biophys Res Commun 750: 151398-151398

PubMed: 39889627 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2025.151398
Primary Citation of Related Structures:
9LJJ

PubMed 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 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.

Organizational Affiliation

HIT Center for Life Sciences, School of Life Science and Technology, Faculty of Life Sciences and Medicine, Harbin Institute of Technology, Harbin, 150001, China.

Macromolecule Content

Total Structure Weight: 84.62 kDa
Atom Count: 5,736
Modeled Residue Count: 728
Deposited Residue Count: 756
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heliorhodopsin	A, B	256	Escherichia coli	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2R4S913 (uncultured Actinomycetes bacterium) Explore A0A2R4S913 Go to UniProtKB: A0A2R4S913
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2R4S913
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody B4	C [auth M], D [auth N]	122	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX2 Query on PX2 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE C₂₇ H₅₂ O₈ P OKLASJZQBDJAPH-RUZDIDTESA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], L [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]