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- PDB-8rsq: Crystal structure of marine actinobacteria clade rhodopsin (MAR) ... -

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Basic information

Entry
Database: PDB / ID: 8rsq
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) - human GTPase Arf1 (L8K,Q71L) chimera; Ground state
ComponentsBacteriorhodopsin,ADP-ribosylation factor 1
KeywordsMEMBRANE PROTEIN / Mac / MacR / MAR / proteorhodopsin / PR / xanthorodopsin / XR / xanthorhodopsin
Function / homology
Function and homology information


mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the plasma membrane / cell leading edge / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / intracellular protein transport / cellular response to virus / neuron projection / postsynaptic density / Golgi membrane / protein domain specific binding / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein ...ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / EICOSANE / RETINAL / ADP-ribosylation factor 1 / Bacteriorhodopsin
Similarity search - Component
Biological speciesCandidatus Actinomarina minuta (bacteria)
Homo sapiens (human)
marine Actinobacteria clade (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBukhdruker, S. / Bratanov, D. / Kovalev, K. / Astashkin, R. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) 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
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 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
Revision 1.2Jul 2, 2025Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin,ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,69711
Polymers45,7091
Non-polymers2,98810
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint9 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.856, 39.718, 94.984
Angle α, β, γ (deg.)90.000, 124.630, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Bacteriorhodopsin,ADP-ribosylation factor 1


Mass: 45709.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria), (gene. exp.) Homo sapiens (human)
Gene: ARF1 / Production host: Escherichia coli (E. coli)
References: UniProt: S5DM51, UniProt: P84077, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Gene: ARF1 / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION / References: small monomeric GTPase
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 2.0 M Ammonium Phosphate buffer

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→37.33 Å / Num. obs: 15145 / % possible obs: 88.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 39.12 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.052 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
6.58-37.332.121.27570.9980.02489.2
2.3-2.411.61.67590.7020.40969.7

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Processing

Software
NameVersionClassification
XDS20210323data reduction
STARANISO2.3.77data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.33 Å / SU ML: 0.3677 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2634 1534 10.14 %
Rwork0.2115 13589 -
obs0.2167 15123 81.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 69 109 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00143239
X-RAY DIFFRACTIONf_angle_d0.45524403
X-RAY DIFFRACTIONf_chiral_restr0.0384492
X-RAY DIFFRACTIONf_plane_restr0.0028550
X-RAY DIFFRACTIONf_dihedral_angle_d12.03551145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.309590.2546431X-RAY DIFFRACTION30.02
2.37-2.460.3024880.2521722X-RAY DIFFRACTION48.62
2.46-2.560.34431320.27291190X-RAY DIFFRACTION79.73
2.56-2.670.32651460.28661368X-RAY DIFFRACTION90.28
2.67-2.820.34251560.25151402X-RAY DIFFRACTION93.69
2.82-2.990.33111570.25321442X-RAY DIFFRACTION96.04
2.99-3.220.30151660.23911438X-RAY DIFFRACTION95.99
3.22-3.550.25941600.20651428X-RAY DIFFRACTION93.69
3.55-4.060.24551500.20031324X-RAY DIFFRACTION87.37
4.06-5.110.20811610.17021409X-RAY DIFFRACTION92.35
5.11-37.330.23081590.18641435X-RAY DIFFRACTION90.11
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29505600896-0.162666438792-0.6936578587042.065077755061.853651495324.177879641090.0956291837878-0.3713601129750.09508625064530.09569012707690.31331622473-0.220997163726-0.102054108920.996063340097-0.2821189276280.3924931280130.0244197750630.06992687112790.516448039903-0.06789002295810.28126743643221.1552530293-9.7357681926236.7489178542
24.09681841353-0.09337305350270.6031291678542.62138635699-0.5089155556983.522395725310.135899555531-0.00120010415466-0.16735843309-0.00708400974239-0.117126918651-0.116498486078-0.1489375726070.306393849198-0.02165560848790.250639820645-0.05625038073190.02606993607940.2004640243340.01815630130690.23808522990448.1922509595-9.804697200630.493728974404
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 215 )2 - 2151 - 208
22chain 'A' and (resid 216 through 396 )216 - 396209 - 389

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