+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2945 | |||||||||
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Title | Structure of lysozyme solved by MicroED to 2.9 A | |||||||||
Map data | Diffraction data phased by molecular replacement (PDB ID: 3J4G) | |||||||||
Sample |
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Keywords | lysozyme | |||||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Shi D / Nannenga BL / Iadanza MG / Gonen T | |||||||||
Citation | Journal: Elife / Year: 2013 Title: Three-dimensional electron crystallography of protein microcrystals. Authors: Dan Shi / Brent L Nannenga / Matthew G Iadanza / Tamir Gonen / Abstract: We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme ...We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1-1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name 'MicroED', that may have wide applicability in structural biology. DOI: http://dx.doi.org/10.7554/eLife.01345.001. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
-Downloads & links
-EMDB archive
Map data | emd_2945.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-2945-v30.xml emd-2945.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | EMD-2945_3J4Gmask.png | 121.7 KB | ||
Filedesc structureFactors | emd_2945_sf.cif.gz | 46.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2945 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2945 | HTTPS FTP |
-Related structure data
Related structure data | 3j4gMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2945.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Diffraction data phased by molecular replacement (PDB ID: 3J4G) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.713 Å / Y: 0.713 Å / Z: 0.685 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hen egg white lysozyme
Entire | Name: Hen egg white lysozyme |
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Components |
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-Supramolecule #1000: Hen egg white lysozyme
Supramolecule | Name: Hen egg white lysozyme / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 14.3 KDa |
-Macromolecule #1: Lysozyme C
Macromolecule | Name: Lysozyme C / type: protein_or_peptide / ID: 1 / Name.synonym: Hen egg white lysozyme / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: egg whites |
Molecular weight | Theoretical: 14.3 KDa |
Sequence | UniProtKB: Lysozyme C |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Concentration | 200 mg/mL |
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Buffer | pH: 4.5 Details: 3.5M sodium chloride; 15% PEG 5,000; 50 mM sodium acetate |
Grid | Details: glow discharged copper grid with holey carbon support |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: blot approximately 10 seconds before plunging |
Details | batch crystallization |
Crystal formation | Details: batch crystallization |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: -45 / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 45 ° |
Temperature | Min: 90 K / Max: 110 K / Average: 100 K |
Details | selected area diffraction |
Date | Jul 1, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2 / Camera length: 1500 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Crystal parameters | Unit cell - A: 77 Å / Unit cell - B: 77 Å / Unit cell - C: 37 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 43 21 2 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |