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- EMDB-15228: RQT-bound 80S ribosome from S. cerevisiae (C1, raw consensus map) -
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Open data
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Basic information
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Title | RQT-bound 80S ribosome from S. cerevisiae (C1, raw consensus map) | ||||||||||||
![]() | refined map of the RQTc1 ribsome | ||||||||||||
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![]() | collision / RNA binding / RQT / RQC / RIBOSOME | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||
![]() | Best KM / Ikeuchi K / Kater L / Best DM / Musial J / Matsuo Y / Berninghausen O / Becker T / Inada T / Beckmann R | ||||||||||||
Funding support | European Union, ![]()
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![]() | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / ![]() ![]() ![]() Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 334.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37.2 KB 37.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.3 KB | Display | ![]() |
Images | ![]() | 104.3 KB | ||
Others | ![]() ![]() | 622.4 MB 622.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 954.7 KB | Display | ![]() |
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Full document | ![]() | 954.3 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | refined map of the RQTc1 ribsome | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: halfmap 1
File | emd_15228_half_map_1.map | ||||||||||||
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Annotation | halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap 2
File | emd_15228_half_map_2.map | ||||||||||||
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Annotation | halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
Entire | Name: ribosome with bound RQT components (Slh1, Cue3 and Rqt4) |
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Components |
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-Supramolecule #1: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
Supramolecule | Name: ribosome with bound RQT components (Slh1, Cue3 and Rqt4) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#82 |
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-Supramolecule #2: RQT complex (Slh1, Cue3 and Rqt4)
Supramolecule | Name: RQT complex (Slh1, Cue3 and Rqt4) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #80-#82 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: ribosome
Supramolecule | Name: ribosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#79 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK II |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |