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- PDB-9jtq: Crystal structure of the light-driven proton pump heimdallarchaei... -

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Basic information

Entry
Database: PDB / ID: 9jtq
TitleCrystal structure of the light-driven proton pump heimdallarchaeial rhodopsin HeimdallR1
ComponentsRhodopsin
KeywordsPROTON TRANSPORT / Rhodopsin / Proton pump
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
NITRATE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesCandidatus Heimdallarchaeota archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMatsuzaki, Y. / Tzlil, G. / Del Carmen Marin, M. / Shihoya, W. / Beja, O. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: To Be Published
Title: Light-harvesting by antenna-containing rhodopsins in pelagic Asgard archaea
Authors: Tzlil, G. / Del Carmen Marin, M. / Matsuzaki, Y. / Nag, P. / Itakura, S. / Mizuno, Y. / Murakoshi, S. / Tanaka, T. / Larom, S. / Konno, M. / Abe-Yoshizumi, R. / Molina-Marquez, A. / Barcenas- ...Authors: Tzlil, G. / Del Carmen Marin, M. / Matsuzaki, Y. / Nag, P. / Itakura, S. / Mizuno, Y. / Murakoshi, S. / Tanaka, T. / Larom, S. / Konno, M. / Abe-Yoshizumi, R. / Molina-Marquez, A. / Barcenas-Perez, D. / Cheel, J. / Koblizek, M. / Leon, R. / Katayama, K. / Kandori, H. / Schapiro, I. / Shihoya, W. / Nureki, O. / Inoue, K. / Rozenberg, A. / Chazan, A. / Beja, O.
History
DepositionOct 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6607
Polymers29,1821
Non-polymers1,4786
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint2 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.590, 60.370, 86.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Rhodopsin


Mass: 29182.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon (archaea)
Gene: CME83_04245 / Production host: Expression vector pET-mod (others) / References: UniProt: A0A2E9CEV6
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 3.9 / Details: PEG 300, sodium acetate, potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.22 Å / Num. obs: 18782 / % possible obs: 99.87 % / Redundancy: 35.8 % / Biso Wilson estimate: 21.87 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 1.054 / Rpim(I) all: 0.1767 / Rrim(I) all: 1.069 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.071 Å / Redundancy: 35 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 1831 / CC1/2: 0.525 / CC star: 0.83 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 940 5.01 %
Rwork0.2011 --
obs0.2028 18773 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 99 115 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032163
X-RAY DIFFRACTIONf_angle_d0.5852919
X-RAY DIFFRACTIONf_dihedral_angle_d10.126340
X-RAY DIFFRACTIONf_chiral_restr0.039317
X-RAY DIFFRACTIONf_plane_restr0.004349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.30311320.2742506X-RAY DIFFRACTION100
2.11-2.240.23021320.22272504X-RAY DIFFRACTION100
2.24-2.410.21871310.18642512X-RAY DIFFRACTION100
2.41-2.650.2231330.17312526X-RAY DIFFRACTION100
2.65-3.040.21511340.17092535X-RAY DIFFRACTION100
3.04-3.830.22191350.18382559X-RAY DIFFRACTION100
3.83-39.220.24241430.21872691X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.6249 Å / Origin y: -13.4984 Å / Origin z: 20.3375 Å
111213212223313233
T0.1609 Å20.0035 Å2-0.0102 Å2-0.1115 Å2-0.0142 Å2--0.1646 Å2
L0.9164 °2-0.0727 °20.1503 °2-0.6055 °2-0.0519 °2--1.7273 °2
S0.0014 Å °-0.0056 Å °0.046 Å °-0.0058 Å °-0.0347 Å °0.0191 Å °-0.0089 Å °-0.0803 Å °0.0194 Å °
Refinement TLS groupSelection details: all

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