9TBE | pdb_00009tbe

Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the K2 state

PDB DOI: https://doi.org/10.2210/pdb9TBE/pdb
EM Map EMD-55766: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Erythrobacter
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-11-19 Released: 2025-12-17
Deposition Author(s): Haubner, M., Williams, H.M., Hruby, J., Straub, M.S., Guskov, A., Kovalev, K., Drabbels, M., Lorenz, U.J.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Microsecond Time-Resolved Cryo-EM Based on Jet Vitrification.

Haubner, M., Williams, H.M., Hruby, J., Straub, M.S., Guskov, A., Kovalev, K., Drabbels, M., Lorenz, U.J.

(2025) bioRxiv

PubMed: 41332690 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1101/2025.11.21.689681
Primary Citation of Related Structures:
9TBD, 9TBE, 9TBF

PubMed 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 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 Er NaR on the microsecond to millisecond timescale. Our experiments significantly expand the ability of cryo-EM to observe protein dynamics across multiple timescales.

Organizational Affiliation

Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015 Lausanne, Switzerland.

Macromolecule Content

Total Structure Weight: 34.95 kDa
Atom Count: 2,380
Modeled Residue Count: 272
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin-like protein	A [auth D]	272	Erythrobacter	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	M [auth D], N [auth D]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain D SDF format, chain E [auth D] SDF format, chain F [auth D] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain G [auth D] SDF format, chain C [auth D] SDF format, chain B [auth D] MOL2 format, chain D MOL2 format, chain E [auth D] MOL2 format, chain F [auth D] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain G [auth D] MOL2 format, chain C [auth D] MOL2 format, chain B [auth D] mmCIF format, chain D mmCIF format, chain E [auth D] mmCIF format, chain F [auth D] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain G [auth D] mmCIF format, chain C [auth D] mmCIF format, chain B [auth D]	B [auth D] C [auth D] D E [auth D] F [auth D] B [auth D], C [auth D], D, E [auth D], F [auth D], G [auth D], H [auth D], I [auth D], J [auth D], K [auth D], L [auth D]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain B [auth D] Focus chain C [auth D] Focus chain D Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain B [auth D] Focus chain C [auth D] Focus chain D Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D]