7AVN | pdb_00007avn

Crystal structure of marine actinobacteria clade rhodopsin (MAR) in the M-like state

PDB DOI: https://doi.org/10.2210/pdb7AVN/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Candidatus Actinomarina minuta
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2020-11-05 Released: 2022-06-01
Deposition Author(s): Gushchin, I., Polovinkin, V., Kovalev, K., Shevchenko, V., Gordeliy, V.
Funding Organization(s): Agence Nationale de la Recherche (ANR), French Infrastructure for Integrated Structural Biology (FRISBI), Grenoble Alliance for Integrated Structural Cell Biology (GRAL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.204 (Depositor), 0.216 (DCC)
R-Value Work:
0.175 (Depositor), 0.186 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.

Bukhdruker, S., Gushchin, I., Shevchenko, V., Kovalev, K., Polovinkin, V., Tsybrov, F., Astashkin, R., Alekseev, A., Mikhaylov, A., Bukhalovich, S., Bratanov, D., Ryzhykau, Y., Kuklina, D., Caramello, N., Rokitskaya, T., Antonenko, Y., Rulev, M., Stoev, C., Zabelskii, D., Round, E., Rogachev, A., Borshchevskiy, V., Ghai, R., Bourenkov, G., Zeghouf, M., Cherfils, J., Engelhard, M., Chizhov, I., Rodriguez-Valera, F., Bamberg, E., Gordeliy, V.

(2025) Sci Adv 11: eadu5303-eadu5303

PubMed: 40238873 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adu5303
Primary Citation Related Structures:
7AVN, 7AVP, 8RSO, 8RSP, 8RSQ, 8RSR, 8RSS, 9G15, 9G16

PubMed Abstract:
Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.

Organizational Affiliation

Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.

Macromolecule Content

Total Structure Weight: 58.61 kDa
Atom Count: 4,017
Modeled Residue Count: 434
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A, B	220	Candidatus Actinomarina minuta	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for S5DM51 (Candidatus Actinomarina minuta) Explore S5DM51 Go to UniProtKB: S5DM51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S5DM51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	HA [auth B], IA [auth B], Q [auth A], R [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Focus chain R [auth A]
OLB Query on OLB Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain P [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain P [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain P [auth A]	GA [auth B], P [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain GA [auth B] Focus chain P [auth A] Interactions & Density Focus chain GA [auth B] Focus chain P [auth A]
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain S [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain S [auth A]	JA [auth B], S [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain JA [auth B] Focus chain S [auth A] Interactions & Density Focus chain JA [auth B] Focus chain S [auth A]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain W [auth B] SDF format, chain O [auth A] SDF format, chain H [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain W [auth B] MOL2 format, chain O [auth A] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain W [auth B] mmCIF format, chain O [auth A] mmCIF format, chain H [auth A]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.204 (Depositor), 0.216 (DCC)
R-Value Work: 0.175 (Depositor), 0.186 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.686	α = 63.66
b = 56.628	β = 78.98
c = 57.386	γ = 80.33

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-19-CE11-0026
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	France	ANR-17-EURE-0003

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 2.0: 2025-04-02
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2025-04-23
Changes: Database references, Structure summary