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Yorodumi- EMDB-5143: Ab initio reconstruction of GroEL via the asymmetric random-model... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5143 | |||||||||
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Title | Ab initio reconstruction of GroEL via the asymmetric random-model method | |||||||||
Map data | GroEL | |||||||||
Sample |
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Keywords | random-model method / ab initio reconstruction / GroEL | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Sanz E / Stewart AB / Belnap DM | |||||||||
Citation | Journal: J Struct Biol / Year: 2010 Title: The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry. Authors: Eduardo Sanz-García / Aaron B Stewart / David M Belnap / Abstract: Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models ...Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models directly from un-averaged, experimental images of asymmetric or symmetric particles. Therefore, the asymmetric RMM can also be used to determine point-group symmetry. The procedure is facilitated by the use of (a) variable angular step-sizes during iterative origin and orientation searches, (b) high numbers of particle images, and (c) highly defocused images. The method is inhibited by mixed-handedness orientation assignments and by particles with inconspicuous features. For symmetric particles, symmetric RMMs can overcome these deficiencies. #1: Journal: J.STRUCT.BIOL. / Year: 2008 Title: A test-bed for optimizing high-resolution single particle reconstructions Authors: Stagg SM / Lander GC / Quispe J / Voss NR / Cheng A / Bradlow H / Bradlow S / Carragher B / Potter CS | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5143.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-5143-v30.xml emd-5143.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | 400_5143.gif 80_5143.gif emd_5143_1.tif | 61.6 KB 6.3 KB 489.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5143 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5143 | HTTPS FTP |
-Validation report
Summary document | emd_5143_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_5143_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_5143_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5143 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5143 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5143.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GroEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GroEL
Entire | Name: GroEL |
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Components |
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-Supramolecule #1000: GroEL
Supramolecule | Name: GroEL / type: sample / ID: 1000 Details: S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. ...Details: S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. Struct. Biol. 163 (2008) 29-39.Publicly available data set. Number unique components: 14 |
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-Supramolecule #1: GroEL
Supramolecule | Name: GroEL / type: organelle_or_cellular_component / ID: 1 / Name.synonym: GroEL Details: S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. ...Details: S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. Struct. Biol. 163 (2008) 29-39.Publicly available data set. Number of copies: 14 / Oligomeric state: homo-tetradecamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: Bacteria / Cell: Escherichia coli |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.2 mg/mL |
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Buffer | pH: 7.5 Details: 100 mM Hepes, pH 7.5, 10 mM Mg(OAc)2, 10 mM KOAc, and 2 mM DTT |
Grid | Details: 400 mesh copper grids Cflat |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Details | S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. Struct. Biol. 163 (2008) 29-39.Publicly available data set. |
Image recording | Category: CCD / Film or detector model: GENERIC CCD Details: S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. ...Details: S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. Struct. Biol. 163 (2008) 29-39.Publicly available data set. |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 9.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | S.M. Stagg, G.C. Lander, J. Quispe, N.R. Voss, A. Cheng, H. Bradlow, S. Bradlow, B. Carragher, C.S. Potter, A test-bed for optimizing high-resolution single particle reconstructions, J. Struct. Biol. 163 (2008) 29-39.Publicly available data set. |
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CTF correction | Details: Phase-flipped |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT3DR, Bsoft Details: Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached. Number images used: 6613 |