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- EMDB-15343: Negative stain EM structure of the compact conformer of kinesin-1... -

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Basic information

Entry
Database: EMDB / ID: EMD-15343
TitleNegative stain EM structure of the compact conformer of kinesin-1 (Kif5C/KLC1).
Map data
Sample
  • Complex: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and kinesin light chain (mouse KLC1A) in the compact conformation
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / negative staining / Resolution: 29.1 Å
AuthorsWeijman JF / Yadav KNS / Surridge KJ / Cross JA / Borucu U / Mantell J / Woolfson DN / Schaffitzel C / Dodding MP
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S000917/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W005581/1 United Kingdom
Wellcome Trust210701/Z/18/Z United Kingdom
Wellcome Trust202904/Z/16/Z United Kingdom
Wellcome Trust206181/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X1 United Kingdom
CitationJournal: 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
DepositionJul 5, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15343.png

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Map

FileDownload / File: emd_15343.map.gz / Format: CCP4 / Size: 561.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 528 pix.
= 554.4 Å		1.05 Å/pix.
x 528 pix.
= 554.4 Å		1.05 Å/pix.
x 528 pix.
= 554.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0051
Minimum - Maximum-0.004043965 - 0.026341384
Average (Standard dev.)6.106391e-06 (±0.0011688313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions528528528
Spacing528528528
CellA=B=C: 554.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15343_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15343_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and k...

EntireName: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and kinesin light chain (mouse KLC1A) in the compact conformation
Components
  • Complex: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and kinesin light chain (mouse KLC1A) in the compact conformation

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Supramolecule #1: Heterotetrameric complex of kinesin heavy chain (rat KIF5C) and k...

SupramoleculeName: 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
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 350 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.003 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeTFS TALOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.4 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 29.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22440
FSC plot (resolution estimation)

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