6CVM

Atomic resolution cryo-EM structure of beta-galactosidase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic Resolution Cryo-EM Structure of beta-Galactosidase.

Bartesaghi, A.Aguerrebere, C.Falconieri, V.Banerjee, S.Earl, L.A.Zhu, X.Grigorieff, N.Milne, J.L.S.Sapiro, G.Wu, X.Subramaniam, S.

(2018) Structure 26: 848

  • DOI: 10.1016/j.str.2018.04.004

  • PubMed Abstract: 
  • The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of me ...

    The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.


    Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D
1021Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lacZ
EC: 3.2.1.23
Find proteins for P00722 (Escherichia coli (strain K12))
Go to UniProtKB:  P00722
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTQ
Query on PTQ

Download SDF File 
Download CCD File 
A, B, C, D
2-phenylethyl 1-thio-beta-D-galactopyranoside
2-Phenylethyl beta-D-thiogalactoside, PETG
C14 H20 O5 S
ZNAMMSOYKPMPGC-HTOAHKCRSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references
  • Version 1.2: 2018-07-18
    Type: Data collection
  • Version 1.3: 2018-08-22
    Type: Data collection, Database references