6IS6 | pdb_00006is6

Crystal structure of Thermoplasmatales archaeon heliorhodopsin

• PDB DOI: https://doi.org/10.2210/pdb6IS6/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Thermoplasmatales archaeon SG8-52-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-15 Released: 2019-09-25 
• Deposition Author(s): Shihoya, W., Yamashita, K., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of heliorhodopsin.

Shihoya, W., Inoue, K., Singh, M., Konno, M., Hososhima, S., Yamashita, K., Ikeda, K., Higuchi, A., Izume, T., Okazaki, S., Hashimoto, M., Mizutori, R., Tomida, S., Yamauchi, Y., Abe-Yoshizumi, R., Katayama, K., Tsunoda, S.P., Shibata, M., Furutani, Y., Pushkarev, A., Beja, O., Uchihashi, T., Kandori, H., Nureki, O.

(2019) Nature 574: 132-136

• PubMed: 31554965 
• DOI: https://doi.org/10.1038/s41586-019-1604-6
• Primary Citation Related Structures: 
  6IS6


• PubMed Abstract: 
  

  Heliorhodopsins (HeRs) are a family of rhodopsins that was recently discovered using functional metagenomics ¹ . They are widely present in bacteria, archaea, algae and algal viruses ^2,3 . Although HeRs have seven predicted transmembrane helices and an all-trans retinal chromophore as in the type-1 (microbial) rhodopsin, they display less than 15% sequence identity with type-1 and type-2 (animal) rhodopsins. HeRs also exhibit the reverse orientation in the membrane compared with the other rhodopsins. Owing to the lack of structural information, little is known about the overall fold and the photoactivation mechanism of HeRs. Here we present the 2.4-Å-resolution structure of HeR from an uncultured Thermoplasmatales archaeon SG8-52-1 (GenBank sequence ID LSSD01000000). Structural and biophysical analyses reveal the similarities and differences between HeRs and type-1 microbial rhodopsins. The overall fold of HeR is similar to that of bacteriorhodopsin. A linear hydrophobic pocket in HeR accommodates a retinal configuration and isomerization as in the type-1 rhodopsin, although most of the residues constituting the pocket are divergent. Hydrophobic residues fill the space in the extracellular half of HeR, preventing the permeation of protons and ions. The structure reveals an unexpected lateral fenestration above the β-ionone ring of the retinal chromophore, which has a critical role in capturing retinal from environment sources. Our study increases the understanding of the functions of HeRs, and the structural similarity and diversity among the microbial rhodopsins.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.
OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.
PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
RIKEN SPring-8 Center, Sayo-gun, Japan.
School of Mathematical and Physical Sciences, Graduate School of Natural Science & Technology, Kanazawa University, Kanazawa, Japan.
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan.
High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.
Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan.
Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.
Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
Department of Physics, Nagoya University, Nagoya, Japan.
Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.
Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan. [e-mail].
OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.16 kDa 
• Atom Count: 2,397 
• Modeled Residue Count: 250 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heliorhodopsin	A	259	Thermoplasmatales archaeon SG8-52-1	Mutation(s): 0
UniProt
Find proteins for A0ACD6B9Z4 (Thermoplasmatales archaeon SG8-52-1) Explore A0ACD6B9Z4  Go to UniProtKB:  A0ACD6B9Z4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth A], P [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)	N [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.3333323

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.98	α = 90
b = 109.35	β = 90
c = 107.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Shihoya, W., Yamashita, K., Nureki, O.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection, Database references
• Version 1.3: 2019-11-20
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary