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- EMDB-55769: Cryo-EM structure of the light-driven sodium pump ErNaR in the mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-55769
TitleCryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the O2 state
Map dataSharpened consensus map
Sample
  • Organelle or cellular component: ErNaR light-driven sodium pump
    • Protein or peptide: Bacteriorhodopsin-like protein
  • Ligand: EICOSANE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: RETINAL
  • Ligand: water
Keywordsrhodopsin / ErNaR / sodium pump / phototransduction / MEMBRANE PROTEIN
Biological speciesErythrobacter (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHaubner M / Williams HM / Hruby J / Straub MS / Guskov A / Kovalev K / Drabbels M / Lorenz UJ
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMCG-2+213773 Switzerland
CitationJournal: bioRxiv / Year: 2025
Title: Microsecond Time-Resolved Cryo-EM Based on Jet Vitrification.
Authors: Michal Haubner / Harry M Williams / Jakub Hruby / Monique S Straub / Albert Guskov / Kirill Kovalev / Marcel Drabbels / Ulrich J Lorenz /
Abstract: Understanding and ultimately predicting the function of proteins is one of the frontiers in structural biology. This will only be possible if it becomes feasible to routinely observe proteins on the ...Understanding and ultimately predicting the function of proteins is one of the frontiers in structural biology. This will only be possible if it becomes feasible to routinely observe proteins on the fast timescales on which they perform their tasks. Recently, laser flash melting and revitrification experiments have improved the time resolution of cryo-electron microscopy (cryo-EM) to microseconds, rendering it fast enough to observe the domain motions of proteins that are frequently linked to function. However, observations have been limited to a time window of just a few hundred microseconds. Here, we introduce time-resolved cryo-EM experiments based on jet vitrification that combine microsecond resolution with an observation window of up to seconds. We use a short laser pulse to initiate protein dynamics, and as they unfold, vitrify the sample with a jet of a liquid cryogen to arrest the dynamics at that point in time. We demonstrate that our approach affords near-atomic spatial resolution and a time resolution of 21 μs. This allows us to observe the photoinduced dynamics of the light-driven sodium pump NaR on the microsecond to millisecond timescale. Our experiments significantly expand the ability of cryo-EM to observe protein dynamics across multiple timescales.
History
DepositionNov 19, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55769.png

Downloads & links

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Map

FileDownload / File: emd_55769.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 278.784 Å		0.73 Å/pix.
x 384 pix.
= 278.784 Å		0.73 Å/pix.
x 384 pix.
= 278.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5570916 - 0.6757173
Average (Standard dev.)0.00035737595 (±0.010196438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 278.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55769_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: Half map A

Fileemd_55769_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55769_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ErNaR light-driven sodium pump

EntireName: ErNaR light-driven sodium pump
Components
  • Organelle or cellular component: ErNaR light-driven sodium pump
    • Protein or peptide: Bacteriorhodopsin-like protein
  • Ligand: EICOSANE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: RETINAL
  • Ligand: water

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Supramolecule #1: ErNaR light-driven sodium pump

SupramoleculeName: ErNaR light-driven sodium pump / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Erythrobacter (bacteria)

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Macromolecule #1: Bacteriorhodopsin-like protein

MacromoleculeName: Bacteriorhodopsin-like protein / type: protein_or_peptide / ID: 1
Details: Bear in mind that LFA and LMT are not part of the sequence here. They derive from the protein solution.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter (bacteria)
Molecular weightTheoretical: 30.676467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPSIENFLAY DFWQYDVIRH LFAFSTAVFL AGLVYFAMTA RTTAPNYRLS ANISAVVMVS AALELGQLWL LWNESFQWAE LQGSFVPVA GERFSNGYRY MNWLIDVPML ATQLVVVCGF VGTELRNRWA KLTIAGVLMI LTGYVGQYFE PAVAGVPGYE G AEQFWIWG ...String:
MPSIENFLAY DFWQYDVIRH LFAFSTAVFL AGLVYFAMTA RTTAPNYRLS ANISAVVMVS AALELGQLWL LWNESFQWAE LQGSFVPVA GERFSNGYRY MNWLIDVPML ATQLVVVCGF VGTELRNRWA KLTIAGVLMI LTGYVGQYFE PAVAGVPGYE G AEQFWIWG IISTAFFVWM LLILANAVRN PQGAPSDEVR SRLKFCFWFL LATWSIYPFA YAMPLFAPTA DGVVVRQVIY TV ADVSSKL VFGVILSQVA LRRSAEEGFE PARVASG

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Macromolecule #2: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 2 / Number of copies: 10 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

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Macromolecule #3: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 3 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #4: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 4 / Number of copies: 1 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 13 / 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

Concentration4.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
10.0 mMC4H11NO3Tris-HCl
0.04 %C24H46On-dodecyl-beta-D-maltoside (DDM)

Details: 10 mM HEPES pH 7.5, 500 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
Details: Grid was sputter coated with 40 nm thick layer of silver beforehand using a Quorum Q300T device.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification carried out using a modified Vitrobot Mark IV, as outlined in the paper reporting this entry..
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0)
Details: Reconstruction conducted in C1 following symmetry expansion of particle stack in C5.
Number images used: 67385
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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