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- PDB-7avn: Crystal structure of marine actinobacteria clade rhodopsin (MAR) ... -

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Basic information

Entry
Database: PDB / ID: 7avn
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the M-like state
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / bacteriorhodopsin / proton pump / ion transport / xanthorhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin
Function and homology information
Biological speciesCandidatus Actinomarina minuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGushchin, I. / Polovinkin, V. / Kovalev, K. / Shevchenko, V. / Gordeliy, V.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0026 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-17-EURE-0003 France
CitationJournal: Sci Adv / Year: 2025
Title: Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.
Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / ...Authors: 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.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Apr 2, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct.title
Revision 2.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,60836
Polymers48,5542
Non-polymers10,05434
Water2,846158
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,30418
Polymers24,2771
Non-polymers5,02717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,30418
Polymers24,2771
Non-polymers5,02717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.686, 56.628, 57.386
Angle α, β, γ (deg.)63.660, 78.980, 80.330
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacteriorhodopsin


Mass: 24277.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5DM51

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Non-polymers , 5 types, 192 molecules

#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H28O
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 1.0 M NH4SO4, 0.1 M NaOAc pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97241 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97241 Å / Relative weight: 1
ReflectionResolution: 1.6→50.98 Å / Num. obs: 59048 / % possible obs: 99.7 % / Redundancy: 10.9 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Net I/σ(I): 23.2 / Num. measured all: 641326 / Scaling rejects: 13
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.892 / Num. unique obs: 2944 / CC1/2: 0.772 / Rpim(I) all: 0.284 / Rrim(I) all: 0.937 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSI

5jsi


Resolution: 1.6→50.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.806 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 3019 5.1 %RANDOM
Rwork0.1754 ---
obs0.1769 56027 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.47 Å2 / Biso mean: 27.59 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20.04 Å2-0.41 Å2
2---0.56 Å2-0.11 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.6→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 335 158 3858
Biso mean--48.58 42.85 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133934
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174054
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.6775271
X-RAY DIFFRACTIONr_angle_other_deg1.4311.6079243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1485488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26721.728162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22915566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2121519
X-RAY DIFFRACTIONr_chiral_restr0.0670.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024151
X-RAY DIFFRACTIONr_gen_planes_other00.02812
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 215 -
Rwork0.239 4161 -
all-4376 -
obs--99.61 %

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