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- EMDB-61685: Cryo-EM structure of the zeaxanthin-bound light-driven proton pum... -

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Basic information

Entry
Database: EMDB / ID: EMD-61685
TitleCryo-EM structure of the zeaxanthin-bound light-driven proton pumping rhodopsin, NM-R1
Map data
Sample
  • Complex: NM-R1
    • Protein or peptide: Proteorhodopsin
  • Ligand: RETINAL
  • Ligand: HEXADECANE
  • Ligand: DODECANE
  • Ligand: Zeaxanthin
  • Ligand: water
Keywordsproton pump rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin / zeaxanthin / MEMBRANE PROTEIN
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / membrane / Proteorhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 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_61685.png

Downloads & links

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Map

FileDownload / File: emd_61685.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.
= 182.6 Å		0.83 Å/pix.
x 220 pix.
= 182.6 Å		0.83 Å/pix.
x 220 pix.
= 182.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.07573628 - 0.13394107
Average (Standard dev.)0.00090804 (±0.006441125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 182.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61685_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61685_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61685_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : NM-R1

EntireName: NM-R1
Components
  • Complex: NM-R1
    • Protein or peptide: Proteorhodopsin
  • Ligand: RETINAL
  • Ligand: HEXADECANE
  • Ligand: DODECANE
  • Ligand: Zeaxanthin
  • Ligand: water

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Supramolecule #1: NM-R1

SupramoleculeName: NM-R1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)

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Macromolecule #1: Proteorhodopsin

MacromoleculeName: Proteorhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Molecular weightTheoretical: 29.481465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNLLLNIEV VRLAADDYVG FTFFVGCMAM MAASAFFFLS MSSFERKWRT SILVSGLITF IAAVHYWYMR DYWSGFAESP VFFRYVDWV LTVPLMCVEF YLILKVAGAK KSLMWKLIFL SVVMLVTGYF GEAVDRGNAW LWGLFSGVAY FWIVIEIWFG K AKKLAVAA ...String:
MNNLLLNIEV VRLAADDYVG FTFFVGCMAM MAASAFFFLS MSSFERKWRT SILVSGLITF IAAVHYWYMR DYWSGFAESP VFFRYVDWV LTVPLMCVEF YLILKVAGAK KSLMWKLIFL SVVMLVTGYF GEAVDRGNAW LWGLFSGVAY FWIVIEIWFG K AKKLAVAA GGDVLAAHKT LCWFVLVGWA IYPIGYMAGT PGWYDSIFGG WDLNVIYNIG DAINKIGFGL VIYNLAVQAT NK KDGLVNL EENLYFQGWS HPQ

UniProtKB: Proteorhodopsin

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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: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 3 / Number of copies: 13 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #4: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 4 / Number of copies: 12 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #5: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 5 / Number of copies: 5 / Formula: K3I
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 51 / 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: 54.0 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: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1814697
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9jou:
Cryo-EM structure of the zeaxanthin-bound light-driven proton pumping rhodopsin, NM-R1

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