+Open data
-Basic information
Entry | Database: PDB / ID: 5vy5 | ||||||
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Title | Rabbit muscle aldolase using 200keV | ||||||
Components | Fructose-bisphosphate aldolase A | ||||||
Keywords | LYASE / glycolytic enzyme | ||||||
Function / homology | Function and homology information negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Herzik Jr., M.A. / Wu, M. / Lander, G.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Methods / Year: 2017 Title: Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV. Authors: Mark A Herzik / Mengyu Wu / Gabriel C Lander / Abstract: Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible ...Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5vy5.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5vy5.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 5vy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vy5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5vy5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5vy5_validation.xml.gz | 275.8 KB | Display | |
Data in CIF | 5vy5_validation.cif.gz | 422.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vy5 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vy5 | HTTPS FTP |
-Related structure data
Related structure data | 8743MC 8741C 8742C 5vy3C 5vy4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10181 (Title: Rabbit muscle aldolase movies obtained using Talos Arctica operating at 200 kV equipped with a K2 Data size: 1.5 TB Data #1: Raw, unaligned movie stacks of rabbit muscle aldolase acquired on a Talos Arctica using a K2 direct electron detector [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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Number of models | 10 |
-Components
#1: Protein | Mass: 39263.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: Muscle / Gene: ALDOA / Production host: Escherichia coli (E. coli) / References: UniProt: P00883, fructose-bisphosphate aldolase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Rabbit Muscle Aldolase / Type: COMPLEX Details: Rabbit Muscle Aldolase (reconstituted from lyophilized form) Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.15 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Specimen was prepared from lyophilized rabbit muscle aldolase (Sigma Aldrich) | |||||||||||||||
Specimen support | Details: 15 Watts / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: 3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 11 sec. / Electron dose: 68 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 810 Details: Images collected using stage position navigation to target exposure. |
Image scans | Sampling size: 5 µm / Width: 7420 / Height: 7676 / Movie frames/image: 44 / Used frames/image: 1-44 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Movies were collected in super-resolution mode and Fourier-binned by two prior to motion correction and dose weighting using MotionCor2 program. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1009341 Details: Template-based particle picking was performed using templates generated from reference-free 2D classification of an initial set of automated particle picks. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83910 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 35 / Protocol: OTHER / Space: REAL / Target criteria: Maximum Likelihood Details: Starting model was generated by stripping PDB entry 6ALD of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting ...Details: Starting model was generated by stripping PDB entry 6ALD of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting weighting/scoring according to estimated map resolution. The top 10 generated models (ranked based on quality metrics) were real-space refined using Phenix software. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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