5A1A

2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb5A1A/pdb
• EM Map EMD-2984: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2015-04-29 Released: 2015-05-06 
• Deposition Author(s): Bartesaghi, A., Merk, A., Banerjee, S., Matthies, D., Wu, X., Milne, J., Subramaniam, S.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with a Cell-Permeant Inhibitor

Bartesaghi, A., Merk, A., Banerjee, S., Matthies, D., Wu, X., Milne, J., Subramaniam, S.

(2015) Science 348: 1147

• PubMed: 25953817 
• DOI: https://doi.org/10.1126/science.aab1576
• Primary Citation of Related Structures:  
  5A1A


• PubMed Abstract: 
  

Cryo-electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM.

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Organizational Affiliation: 

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 467.06 kDa 
• Atom Count: 33,696 
• Modelled Residue Count: 4,088 
• Deposited Residue Count: 4,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GALACTOSIDASE	A, B, C, D	1,022	Escherichia coli K-12	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTQ	E [auth A], J [auth B], O [auth C], T [auth D]	2-phenylethyl 1-thio-beta-D-galactopyranoside C14 H20 O5 S ZNAMMSOYKPMPGC-HTOAHKCRSA-N
MG	F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], U [auth D], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Bartesaghi, A., Merk, A., Banerjee, S., Matthies, D., Wu, X., Milne, J., Subramaniam, S.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2015-05-20
  Changes: Database references
• Version 1.3: 2015-06-24
  Changes: Database references
• Version 1.4: 2018-10-03
  Changes: Data collection