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Yorodumi- EMDB-15343: Negative stain EM structure of the compact conformer of kinesin-1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15343 | |||||||||||||||||||||
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Title | Negative stain EM structure of the compact conformer of kinesin-1 (Kif5C/KLC1). | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Biological species | Rattus norvegicus (Norway rat) | |||||||||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 29.1 Å | |||||||||||||||||||||
Authors | Weijman JF / Yadav KNS / Surridge KJ / Cross JA / Borucu U / Mantell J / Woolfson DN / Schaffitzel C / Dodding MP | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Molecular architecture of the autoinhibited kinesin-1 lambda particle. Authors: Johannes F Weijman / Sathish K N Yadav / Katherine J Surridge / Jessica A Cross / Ufuk Borucu / Judith Mantell / Derek N Woolfson / Christiane Schaffitzel / Mark P Dodding / Abstract: Despite continuing progress in kinesin enzyme mechanochemistry and emerging understanding of the cargo recognition machinery, it is not known how these functions are coupled and controlled by the α- ...Despite continuing progress in kinesin enzyme mechanochemistry and emerging understanding of the cargo recognition machinery, it is not known how these functions are coupled and controlled by the α-helical coiled coils encoded by a large component of kinesin protein sequences. Here, we combine computational structure prediction with single-particle negative-stain electron microscopy to reveal the coiled-coil architecture of heterotetrameric kinesin-1 in its compact state. An unusual flexion in the scaffold enables folding of the complex, bringing the kinesin heavy chain-light chain interface into close apposition with a tetrameric assembly formed from the region of the molecule previously assumed to be the folding hinge. This framework for autoinhibition is required to uncover how engagement of cargo and other regulatory factors drives kinesin-1 activation. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15343.map.gz | 524.4 MB | EMDB map data format | |
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Header (meta data) | emd-15343-v30.xml emd-15343.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15343_fsc.xml | 19 KB | Display | FSC data file |
Images | emd_15343.png | 28 KB | ||
Others | emd_15343_half_map_1.map.gz emd_15343_half_map_2.map.gz | 450.6 MB 451.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15343 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15343 | HTTPS FTP |
-Validation report
Summary document | emd_15343_validation.pdf.gz | 626.3 KB | Display | EMDB validaton report |
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Full document | emd_15343_full_validation.pdf.gz | 625.8 KB | Display | |
Data in XML | emd_15343_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_15343_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15343 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15343 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15343.map.gz / Format: CCP4 / Size: 561.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15343_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15343_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and k...
Entire | Name: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and kinesin light chain (mouse KLC1A) in the compact conformation |
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Components |
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-Supramolecule #1: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and k...
Supramolecule | Name: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and kinesin light chain (mouse KLC1A) in the compact conformation type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 350 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.003 mg/mL |
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Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: Uranyl Acetate |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.4 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |