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- PDB-7ytb: Crystal structure of Kin4B8 -

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Basic information

Entry
Database: PDB / ID: 7ytb
TitleCrystal structure of Kin4B8
ComponentsKin4B8
KeywordsMEMBRANE PROTEIN / rhodopsin / inward proton pump
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL
Function and homology information
Biological speciesBdellovibrio (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsMurakoshi, S. / Chazan, A. / Shihoya, W. / Beja, O. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nature / Year: 2023
Title: Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.
Authors: Ariel Chazan / Ishita Das / Takayoshi Fujiwara / Shunya Murakoshi / Andrey Rozenberg / Ana Molina-Márquez / Fumiya K Sano / Tatsuki Tanaka / Patricia Gómez-Villegas / Shirley Larom / Alina ...Authors: Ariel Chazan / Ishita Das / Takayoshi Fujiwara / Shunya Murakoshi / Andrey Rozenberg / Ana Molina-Márquez / Fumiya K Sano / Tatsuki Tanaka / Patricia Gómez-Villegas / Shirley Larom / Alina Pushkarev / Partha Malakar / Masumi Hasegawa / Yuya Tsukamoto / Tomohiro Ishizuka / Masae Konno / Takashi Nagata / Yosuke Mizuno / Kota Katayama / Rei Abe-Yoshizumi / Sanford Ruhman / Keiichi Inoue / Hideki Kandori / Rosa León / Wataru Shihoya / Susumu Yoshizawa / Mordechai Sheves / Osamu Nureki / Oded Béjà /
Abstract: Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium and a ...Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium and a terrestrial cyanobacterium. Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps from marine photoheterotrophs have thus far failed. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.
History
DepositionAug 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kin4B8
B: Kin4B8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,20010
Polymers57,4922
Non-polymers2,7088
Water45025
1
A: Kin4B8
B: Kin4B8
hetero molecules

A: Kin4B8
B: Kin4B8
hetero molecules

A: Kin4B8
B: Kin4B8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,59930
Polymers172,4756
Non-polymers8,12424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23350 Å2
ΔGint-152 kcal/mol
Surface area58300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.030, 100.030, 116.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Kin4B8


Mass: 28745.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-RET / RETINAL


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


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: PEG550MME, potassium thiocyanate, HEPES-NaOH

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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: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.27 Å / Num. obs: 13912 / % possible obs: 99.51 % / Redundancy: 23 % / Biso Wilson estimate: 67.55 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.5168 / Rpim(I) all: 0.1049 / Rrim(I) all: 0.5285 / Net I/σ(I): 10.25
Reflection shellResolution: 3→3.107 Å / Redundancy: 24 % / Rmerge(I) obs: 8.544 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 1332 / CC1/2: 0.378 / CC star: 0.741 / Rpim(I) all: 1.733 / Rrim(I) all: 8.736 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.27 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 697 5.03 %
Rwork0.2165 --
obs0.2185 13860 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 183 25 4106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034219
X-RAY DIFFRACTIONf_angle_d0.685710
X-RAY DIFFRACTIONf_dihedral_angle_d13.1091545
X-RAY DIFFRACTIONf_chiral_restr0.038647
X-RAY DIFFRACTIONf_plane_restr0.005676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.34341320.28282572X-RAY DIFFRACTION99
3.23-3.560.32671350.23812605X-RAY DIFFRACTION100
3.56-4.070.25711420.21872609X-RAY DIFFRACTION100
4.07-5.120.22261400.19072629X-RAY DIFFRACTION100
5.13-48.270.22941480.21022748X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.9081 Å / Origin y: 48.7132 Å / Origin z: 28.9104 Å
111213212223313233
T0.3015 Å20.0922 Å20.0248 Å2-0.4312 Å20.0198 Å2--0.3902 Å2
L1.55 °20.4226 °20.043 °2-1.5018 °20.2343 °2--1.4393 °2
S-0.0124 Å °0.0644 Å °-0.1382 Å °-0.021 Å °0.0109 Å °-0.207 Å °0.1134 Å °0.3881 Å °0.0143 Å °
Refinement TLS groupSelection details: all

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