9HKI | pdb_00009hki

Plunge-frozen beta-galactosidase

PDB DOI: https://doi.org/10.2210/pdb9HKI/pdb
EM Map EMD-52230: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-03 Released: 2025-12-17
Deposition Author(s): Barrass, S.V., Esser, T.K., Mowry, N.J., Eriksson, L., Hruby, J., Seeley, L.T., Drabbels, M., Baker, L.A., Rauschenbach, S., Lorenz, U.J.
Funding Organization(s): Swiss National Science Foundation, UK Research and Innovation (UKRI), Biotechnology and Biological Sciences Research Council (BBSRC), H2020 Marie Curie Actions of the European Commission, Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM sample preparation with soft-landing and laser flash melting.

Barrass, S.V., Esser, T.K., Mowry, N.J., Eriksson, L., Wenz, J., Seeley, L.T., Curtis, W.A., Baker, L.A., Drabbels, M., Rauschenbach, S., Lorenz, U.J.

(2026) Nat Commun 17

PubMed: 42881156 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-77723-6
Primary Citation Related Structures:
9HKI, 9HLM

PubMed Abstract:
The preparation of cryo-EM samples by soft-landing mass spectrometry promises to significantly simplify sample optimization, which has remained an important bottleneck in single-particle cryo-electron microscopy (cryo‑EM). However, only compacted configurations are observed after soft-landing since the proteins are dehydrated in the process. Here, we deposit a layer of amorphous ice onto the sample and briefly flash melt it to rehydrate the soft-landed proteins. Melting with a 30 µs laser pulse creates a broad ensemble of partially rehydrated structures. However, a subset of particles returns to a configuration close to the native state. This allows us to propose strategies to fully rehydrate the entire ensemble and brings routine sample preparation by soft-landing mass spectrometry within reach.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 465.25 kDa
Atom Count: 36,752
Modeled Residue Count: 4,084
Deposited Residue Count: 4,084
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,021	Escherichia coli	Mutation(s): 0 Gene Names: lacZ, b0344, JW0335 EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722 Go to UniProtKB: P00722
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00722
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	213773
Swiss National Science Foundation	Switzerland	207842
UK Research and Innovation (UKRI)	United Kingdom	EP/V051474/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V019694/1
H2020 Marie Curie Actions of the European Commission	European Union	883387
Wellcome Trust	United Kingdom	218482/Z/19/Z