9HLM | pdb_00009hlm

Soft-landed and rehydrated beta-galactosidase (best particles)

• PDB DOI: https://doi.org/10.2210/pdb9HLM/pdb
• EM Map EMD-52260: EMDB EMDataResource

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


• Deposited: 2024-12-05 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: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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 
• 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.
Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford, UK.
Thermo Fisher Scientific, De Schakel 2, Eindhoven, Noord-Brabant, The Netherlands.
Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK.
Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Ultrafast X-ray Sciences, Lausanne, Switzerland.
Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK.
Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, Lausanne, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 464.96 kDa 
• Atom Count: 32,040 
• Modeled Residue Count: 3,984 
• Deposited Residue Count: 4,084 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.5

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 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	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

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-09-23
  Changes: Data collection, Database references
• Version 1.2: 2026-10-28
  Changes: Data collection, Database references