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- PDB-9jow: Cryo-EM structure of the myxol-bound light-driven chloride ion-pu... -

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Basic information

Entry
Database: PDB / ID: 9jow
TitleCryo-EM structure of the myxol-bound light-driven chloride ion-pumping rhodopsin, NM-R3
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / chloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Octadecane / : / TETRADECANE / DECANE / DODECANE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DIUNDECYL PHOSPHATIDYL CHOLINE / HEXADECANE / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsHosaka, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Intracellular carotenoids enhance the pump activation of microbial rhodopsin in two ways: The light-harvesting antenna and the photocycle acceleration
Authors: Fujiwara, T. / Hosaka, T. / Hasegawa-Takano, M. / Nishimura, Y. / Tominaga, K. / Mori, K. / Nishino, S. / Kawasaki, Y. / Takahashi, Y. / Uchikubo-Kamo, T. / Hanada, K. / Takaichi, S. / ...Authors: Fujiwara, T. / Hosaka, T. / Hasegawa-Takano, M. / Nishimura, Y. / Tominaga, K. / Mori, K. / Nishino, S. / Kawasaki, Y. / Takahashi, Y. / Uchikubo-Kamo, T. / Hanada, K. / Takaichi, S. / Inoue, K. / Shirouzu, M. / Yoshizawa, S.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloride pumping rhodopsin
B: Chloride pumping rhodopsin
C: Chloride pumping rhodopsin
D: Chloride pumping rhodopsin
E: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,41959
Polymers153,5555
Non-polymers16,86454
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Chloride pumping rhodopsin


Mass: 30710.936 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3

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Non-polymers , 11 types, 241 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1L4O / (3~{S},4~{Z},6~{E},8~{Z},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]pentacosa-4,6,8,10,12,14,16,18,20,22,24-undecaene-2,3-diol


Mass: 584.871 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NM-R3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60.425 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 791219 / Symmetry type: POINT
RefinementResolution: 2.48→2.48 Å / Cor.coef. Fo:Fc: 0.833 / SU B: 4.051 / SU ML: 0.08 / ESU R: 0.205
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.28332 --
obs0.28332 165207 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 101.513 Å2
Refinement stepCycle: 1 / Total: 11677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.01211711
ELECTRON MICROSCOPYr_bond_other_d00.01612118
ELECTRON MICROSCOPYr_angle_refined_deg2.1311.79815727
ELECTRON MICROSCOPYr_angle_other_deg0.8421.69427773
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.79951315
ELECTRON MICROSCOPYr_dihedral_angle_2_deg16.314585
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.098101700
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1090.21740
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.0212760
ELECTRON MICROSCOPYr_gen_planes_other0.0080.022750
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it10.8118.5675275
ELECTRON MICROSCOPYr_mcbond_other10.7738.5655274
ELECTRON MICROSCOPYr_mcangle_it12.12215.4546585
ELECTRON MICROSCOPYr_mcangle_other12.12115.4556586
ELECTRON MICROSCOPYr_scbond_it15.85910.8426436
ELECTRON MICROSCOPYr_scbond_other15.85810.8436437
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other21.84919.269143
ELECTRON MICROSCOPYr_long_range_B_refined23.68586.5113143
ELECTRON MICROSCOPYr_long_range_B_other23.68486.5113144
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.609 12317 -
obs--100 %

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