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

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Basic information

Entry
Database: PDB / ID: 8rsp
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the P596 state
ComponentsMicrobial rhodopsin
KeywordsMEMBRANE PROTEIN / Mac / MacR / MAR / proteorhodopsin / PR / xanthorodopsin / XR / xanthorhodopsin
Function / homologyEICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / RETINAL
Function and homology information
Biological speciesmarine Actinobacteria clade (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBukhdruker, S. / 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

Downloads & links

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Assembly

Deposited unit
A: Microbial rhodopsin
B: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29833
Polymers48,5542
Non-polymers8,74431
Water99155
1
A: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,88118
Polymers24,2771
Non-polymers4,60417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,41715
Polymers24,2771
Non-polymers4,14014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.684, 55.982, 56.728
Angle α, β, γ (deg.)64.410, 81.310, 84.430
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Microbial rhodopsin


Mass: 24277.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 86 molecules

#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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.) marine Actinobacteria clade (bacteria) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.8 / Details: 3.0 M Ammonium Phosphate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9755 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.41→40.19 Å / Num. obs: 52344 / % possible obs: 79.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.28 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 11.5
Reflection shell

Num. unique obs: 2662 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Rpim(I) all% possible all
4.38-40.193.843.60.9990.01592.6
1.41-1.543.90.70.2851.06945

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Processing

Software
NameVersionClassification
XDS20220110data reduction
STARANISO2.3.89data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→40.19 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 40.9277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2607 2403 4.68 %
Rwork0.2323 48904 -
obs0.2337 51307 59.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.32 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 259 55 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633877
X-RAY DIFFRACTIONf_angle_d0.77285214
X-RAY DIFFRACTIONf_chiral_restr0.0635553
X-RAY DIFFRACTIONf_plane_restr0.0056634
X-RAY DIFFRACTIONf_dihedral_angle_d13.37891444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.440.183120.4096107X-RAY DIFFRACTION2.16
1.44-1.470.3949210.3468476X-RAY DIFFRACTION9.8
1.47-1.50.4936220.4036834X-RAY DIFFRACTION16.84
1.5-1.540.3357570.32921179X-RAY DIFFRACTION24.43
1.54-1.580.32921020.32731860X-RAY DIFFRACTION38.51
1.58-1.630.33791010.31422436X-RAY DIFFRACTION50.17
1.63-1.680.311450.31932853X-RAY DIFFRACTION59.25
1.68-1.740.30651860.31223146X-RAY DIFFRACTION65.41
1.74-1.810.31052040.29873467X-RAY DIFFRACTION72.01
1.81-1.890.33121980.3163674X-RAY DIFFRACTION76.79
1.89-1.990.37741690.3923278X-RAY DIFFRACTION67.93
1.99-2.120.25422110.24644330X-RAY DIFFRACTION88.54
2.12-2.280.38341350.30563752X-RAY DIFFRACTION76.53
2.28-2.510.24431670.22564271X-RAY DIFFRACTION87.45
2.51-2.870.24091940.21574432X-RAY DIFFRACTION90.65
2.87-3.620.25952550.20694391X-RAY DIFFRACTION91.84
3.62-40.190.22182340.19194418X-RAY DIFFRACTION91.38
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)
11.394685492331.10186609133-0.1965291765861.314122018261.030870623791.74387694126-0.04251475472370.0231642139351-0.3346197893520.203648320676-0.4229558989820.1648052421960.1929177210290.110358419154-0.5279076762530.219227489104-0.03801656517710.02703145085280.200852060577-0.02577984292190.340586601421-13.538713975-5.345242050773.86311219776
22.927112679070.0447787714499-0.05615843926731.144991904711.551977225423.34597879269-0.004304162627530.173404969459-0.432722727989-0.686861083042-0.1477024242880.562372025013-0.167908914844-0.107659599484-0.2700716030530.171037833446-0.006103764283-0.03295615917510.149193443562-0.07089045448470.147999431243-9.87996834594-3.19870633938-4.30925047479
31.03287934866-0.153524654058-0.1363038177730.369107819330.8465643488411.657943540190.1813223993830.102175851447-0.216377108021-0.246173764499-0.2587542322750.3334618875010.186223985199-0.268326260621-0.01699500529180.219183099914-0.0265651780940.03705594637210.267267556869-0.1037961916970.220798091995-0.304729788898-2.58008262227-3.50143001664
41.259311201130.1603748486710.121530739461.800092020010.8894114925950.8989644300550.1257679920950.1360899845190.118391187593-0.700263860875-0.252934600032-0.72570749267-0.1840267542730.2013966788350.02797527001360.2561456832740.02017072780470.05865492441190.1976281802640.006383617510040.2170810454827.821618625741.24451003973-8.35976975456
51.308694034480.450916849546-0.06179828060951.0189997727-0.3188184187491.401330229550.222861694773-0.0642711723592-0.208342762055-0.450624159129-0.1524299966290.21471353403-0.06231192494670.2033590389680.08582263439740.128835434058-0.01067459180080.0001447104198610.137679620790.04382802172330.27326651433412.93263420380.01369124081441.02673192859
61.08415818818-0.359845417296-0.7429899268150.9960958183540.9876853334770.767749726976-0.0777833051186-0.3842842164370.2010480682270.0001814116497470.238988565977-0.405800233175-0.2084215677940.1136262985260.09611382622250.248538211901-0.02660559077130.01000576286680.2512677366-0.04183069655740.2144773351443.34141393364.634658307667.12849985207
71.160520449291.004110098520.05247019784891.274771437621.057795267631.477219694110.0125427497954-0.168569732501-0.08895408221340.15434232752-0.03759241742390.0629678306335-0.148446372753-0.068642594317-0.06255864501280.2402978542330.03164198508150.01253146052190.158753515785-0.03547655579570.178433387242-4.89132920712.303621167774.25402473988
81.40785381948-0.50326796551.175653391230.3000213964560.2280672452392.03533628702-0.0267437076078-0.268537082373-0.131408234219-0.205603356469-0.169328445966-0.1257116151060.1724471533710.3330611560310.007101693383710.1539321090530.0223680435760.00863652999760.2590337173820.05459550151530.191826816561.04181501266-18.9419676342-22.7427932627
92.547064355760.04782199381780.5024176560311.170044884031.73205105252.965207382290.0248405805816-0.271704893471-0.147303294960.567113951347-0.195416937844-0.510655842303-0.6083248813310.176976679694-0.08414118935850.168420335381-0.001776453952340.001920934119090.159664093773-0.0460021256650.07665670426-3.16483240083-13.1691384309-17.7522484103
102.20559832628-0.6222395479711.332351293380.8552351728731.022307826173.344501580520.107199546312-0.2998929763350.0303709748177-0.1669392236090.07872724277340.0637233254277-0.309644192447-0.08253069331420.2241735281630.1321294990890.03447279660740.0314649666430.282661366484-0.03340727971510.142019893457-16.6758487822-8.6418490308-18.8977953124
111.35896609162-0.377110402890.4635238918760.9667254316050.8643161046751.182989516370.134800712225-0.1509144504420.0118923991952-0.274502958699-0.1187557462680.258628335789-0.0722506820901-0.474016615037-0.09552711467750.1476995181820.05926492311960.0001646588669560.2486065523810.07227139179590.269227374824-25.1142978009-11.103996179-25.5645978691
120.709976750601-0.4300838910920.002255888817330.5088287097620.3135469016980.5509206750050.136380981120.007997936565980.212066402549-0.3137188191580.04119282280530.0908155887134-0.743113239197-0.4823712937770.03737366873790.3775484426240.03788809186880.04821733273020.272087202283-0.01046651427170.161306600133-11.4582615777-4.47475452363-37.0458884885
131.23035677934-0.8176780374020.3335576624270.313314562569-0.08532732229291.04773399444-0.04249470840210.0583494786381-0.313659731138-0.3251948287080.1247546740140.0686986410380.159842589184-0.04895201732510.0116943482330.231664339323-0.0230981418989-0.02204985950590.1626085594760.00169372087080.166923080393-11.3495696149-16.6894953345-27.5378133443
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 29 )AA1 - 291 - 29
22chain 'A' and (resid 30 through 61 )AA30 - 6130 - 61
33chain 'A' and (resid 62 through 90 )AA62 - 9062 - 90
44chain 'A' and (resid 91 through 116 )AA91 - 11691 - 116
55chain 'A' and (resid 117 through 149 )AA117 - 149117 - 149
66chain 'A' and (resid 150 through 184 )AA150 - 184150 - 184
77chain 'A' and (resid 185 through 216 )AA185 - 216185 - 216
88chain 'B' and (resid 1 through 29 )BS1 - 291 - 29
99chain 'B' and (resid 30 through 65 )BS30 - 6530 - 65
1010chain 'B' and (resid 66 through 122 )BS66 - 12266 - 122
1111chain 'B' and (resid 123 through 149 )BS123 - 149123 - 149
1212chain 'B' and (resid 150 through 168 )BS150 - 168150 - 168
1313chain 'B' and (resid 169 through 217 )BS169 - 217169 - 217

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