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- EMDB-61687: Cryo-EM structure of the myxol-bound light-driven chloride ion-pu... -

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Basic information

Entry
Database: EMDB / ID: EMD-61687
TitleCryo-EM structure of the myxol-bound light-driven chloride ion-pumping rhodopsin, NM-R3
Map data
Sample
  • Complex: NM-R3
    • Protein or peptide: x 1 types
  • Ligand: x 11 types
Keywordschloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin / MEMBRANE PROTEIN
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / membrane / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsHosaka T / Shirouzu M
Funding support Japan, 1 items
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 / Inoue K / Shirouzu M / Yoshizawa S
History
DepositionSep 25, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61687.png

Downloads & links

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Map

FileDownload / File: emd_61687.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 220 pix.
= 182.27 Å		0.83 Å/pix.
x 220 pix.
= 182.27 Å		0.83 Å/pix.
x 220 pix.
= 182.27 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042
Minimum - Maximum-0.05022373 - 0.12722413
Average (Standard dev.)0.0011104569 (±0.0079644285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 182.26999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61687_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61687_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_61687_half_map_2.map
Projections & Slices
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Sample components

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Entire : NM-R3

EntireName: NM-R3
Components
  • Complex: NM-R3
    • Protein or peptide: Chloride pumping rhodopsin
  • Ligand: RETINAL
  • Ligand: (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
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: HEXADECANE
  • Ligand: Octadecane
  • Ligand: DODECANE
  • Ligand: TETRADECANE
  • Ligand: DECANE
  • Ligand: water

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Supramolecule #1: NM-R3

SupramoleculeName: NM-R3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)

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Macromolecule #1: Chloride pumping rhodopsin

MacromoleculeName: Chloride pumping rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Molecular weightTheoretical: 30.710936 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSGSSGMKN IESLFDYSAG QFEFIDHLLT MGVGVHFAAL IFFLVVSQFV APKYRIATAL SCIVMVSAGL ILNSQAVMWT DAYAYVDGS YQLQDLTFSN GYRYVNWMAT IPCLLLQLLI VLNLKGKELF STATWLILAA WGMIITGYVG QLYEVDDIAQ L MIWGAVST ...String:
GSSGSSGMKN IESLFDYSAG QFEFIDHLLT MGVGVHFAAL IFFLVVSQFV APKYRIATAL SCIVMVSAGL ILNSQAVMWT DAYAYVDGS YQLQDLTFSN GYRYVNWMAT IPCLLLQLLI VLNLKGKELF STATWLILAA WGMIITGYVG QLYEVDDIAQ L MIWGAVST AFFVVMNWIV GTKIFKNRAT MLGGTDSTIT KVFWLMMFAW TLYPIAYLVP AFMNNADGVV LRQLLFTIAD IS SKVIYGL MITYIAIQQS AAAGYVPAQQ ALGRIGMDSK AA

UniProtKB: Chloride pumping rhodopsin

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 5 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #3: (3~{S},4~{Z},6~{E},8~{Z},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E...

MacromoleculeName: (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- ...Name: (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
type: ligand / ID: 3 / Number of copies: 5 / Formula: A1L4O
Molecular weightTheoretical: 584.871 Da

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 5 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 6 / Number of copies: 5 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #7: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 7 / Number of copies: 11 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #8: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 8 / Number of copies: 3 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

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Macromolecule #9: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 9 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #10: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 10 / Number of copies: 6 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #11: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 11 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 187 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.425 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5b2n

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 791219
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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