[English] 日本語
Yorodumi- PDB-5a1a: 2.2 A resolution cryo-EM structure of beta-galactosidase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a1a | ||||||
---|---|---|---|---|---|---|---|
Title | 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor | ||||||
Components | BETA-GALACTOSIDASE | ||||||
Keywords | HYDROLASE / NEAR-ATOMIC / NEAR-ATOMIC RESOLUTION CRYO-ELECTRON MICROSCOPY / SINGLE- PARTICLE CRYO-EM / PROTEIN COMPLEXES / PETG | ||||||
Function / homology | Function and homology information alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
Authors | Bartesaghi, A. / Merk, A. / Banerjee, S. / Matthies, D. / Wu, X. / Milne, J. / Subramaniam, S. | ||||||
Citation | Journal: Science / Year: 2015 Title: 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor. Authors: Alberto Bartesaghi / Alan Merk / Soojay Banerjee / Doreen Matthies / Xiongwu Wu / Jacqueline L S Milne / Sriram Subramaniam / 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- ...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. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5a1a.cif.gz | 813.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a1a.ent.gz | 656.1 KB | Display | PDB format |
PDBx/mmJSON format | 5a1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a1a_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5a1a_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5a1a_validation.xml.gz | 123 KB | Display | |
Data in CIF | 5a1a_validation.cif.gz | 179.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/5a1a ftp://data.pdbj.org/pub/pdb/validation_reports/a1/5a1a | HTTPS FTP |
-Related structure data
Related structure data | 2984MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10061 (Title: 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor Data size: 12.4 TB Data #1: Averages of aligned movie frames [micrographs - single frame] Data #2: Raw movie frames [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 116370.188 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P00722, beta-galactosidase #2: Sugar | ChemComp-PTQ / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ESCHERICHIA COLI BETA- GALACTOSIDASE WITH PETG / Type: COMPLEX |
---|---|
Buffer solution | Name: 25 MM TRIS, PH 8.0, 50 MM NACL, 2 MM MGCL2, 0.5 MM TCEP pH: 8 Details: 25 MM TRIS, PH 8.0, 50 MM NACL, 2 MM MGCL2, 0.5 MM TCEP |
Specimen | Conc.: 2.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE Details: BLOT FOR 2 SECONDS BEFORE PLUNGING INTO LIQUID ETHANE (LEICA EM GP). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Date: Dec 15, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 215000 X / Calibrated magnification: 215000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 79.7 K |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
Image scans | Num. digital images: 1487 |
-Processing
EM software | Name: FREALIGN / Category: 3D reconstruction | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||
3D reconstruction | Resolution: 2.2 Å / Num. of particles: 41123 / Nominal pixel size: 0.637 Å / Actual pixel size: 0.637 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2984. (DEPOSITION ID: 13171). Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 2.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
|