[English] 日本語
Yorodumi
- PDB-8rsp: Crystal structure of marine actinobacteria clade rhodopsin (MAR) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rsp
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the P596 state
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / Mac / MacR / MAR / proteorhodopsin / PR / xanthorodopsin / XR / xanthorhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / RETINAL / Bacteriorhodopsin
Function and homology information
Biological speciesCandidatus Actinomarina minuta (bacteria)
marine 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
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.pdbx_gene_src_ncbi_taxonomy_id ..._entity.pdbx_description / _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_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


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

-
Components

-
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 (E. coli) / References: UniProt: S5DM51

-
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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more