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

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Basic information

Entry
Database: PDB / ID: 8rsr
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) - human GTPase Arf1 (L8K,Q71L) chimera; N state
ComponentsMicrobial rhodopsin - GTPase chimera,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 / cell leading edge / Synthesis of PIPs at the plasma membrane / 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 / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / small GTPase Arf family 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / EICOSANE / OLEIC ACID / RETINAL / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesmarine 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microbial rhodopsin - GTPase chimera,ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0025
Polymers45,7091
Non-polymers1,2934
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-1 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.186, 39.787, 95.756
Angle α, β, γ (deg.)90.000, 124.540, 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

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Protein , 1 types, 1 molecules A

#1: Protein Microbial rhodopsin - GTPase chimera,ADP-ribosylation factor 1


Mass: 45709.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Gene: ARF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84077, small monomeric GTPase

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Non-polymers , 5 types, 111 molecules

#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.: 1 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 2.0 M Ammonium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.1→39.44 Å / Num. obs: 19820 / % possible obs: 93 % / Redundancy: 3 % / Biso Wilson estimate: 48.48 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.9 %

Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
6.17-39.4422.49900.9970.02495.2
2.1-2.190.69920.1721.27971.5

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Processing

Software
NameVersionClassification
XDS20220820data reduction
STARANISO2.3.91data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.44 Å / SU ML: 0.3838 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.8623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2822 1730 10.06 %
Rwork0.2516 15473 -
obs0.2547 17203 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 53 107 3111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163103
X-RAY DIFFRACTIONf_angle_d0.46454227
X-RAY DIFFRACTIONf_chiral_restr0.0385475
X-RAY DIFFRACTIONf_plane_restr0.0023528
X-RAY DIFFRACTIONf_dihedral_angle_d11.86821081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.35621170.3409912X-RAY DIFFRACTION67.52
2.37-2.440.32711170.33071066X-RAY DIFFRACTION77.17
2.44-2.530.36591180.33061191X-RAY DIFFRACTION84.62
2.53-2.630.3471500.32761311X-RAY DIFFRACTION93.41
2.63-2.750.35351540.33121341X-RAY DIFFRACTION97.33
2.75-2.90.34071580.33271385X-RAY DIFFRACTION98.53
2.9-3.080.35371540.29361374X-RAY DIFFRACTION98.58
3.08-3.320.31651550.28691398X-RAY DIFFRACTION98.79
3.32-3.650.30361480.24991377X-RAY DIFFRACTION97.76
3.65-4.180.22931400.23191289X-RAY DIFFRACTION91.78
4.18-5.260.25231570.20031407X-RAY DIFFRACTION98.61
5.26-39.440.23891620.20891422X-RAY DIFFRACTION95.83
Refinement TLS params.Method: refined / Origin x: -32.2939728208 Å / Origin y: 9.7638206207 Å / Origin z: 19.2490964669 Å
111213212223313233
T0.431308749514 Å2-0.0298366446248 Å2-0.0508723889862 Å2-0.417420789796 Å2-0.0257865427245 Å2--0.395446491242 Å2
L2.40595205793 °2-0.0786321692064 °2-2.31528946182 °2-0.352080392591 °20.0371992346039 °2--2.60884121035 °2
S0.0482433482884 Å °-0.452332968476 Å °0.0811481897034 Å °0.153525619908 Å °0.0333873505111 Å °-0.146758586574 Å °-0.0960481182865 Å °0.41653923193 Å °-0.00958601750683 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 396)

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