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- EMDB-48092: Consensus map of full-length human dynein-1 in phi-like conformat... -

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Basic information

Entry
Database: EMDB / ID: EMD-48092
TitleConsensus map of full-length human dynein-1 in phi-like conformation bound to a Lis1 dimer under Nde1-Lis1 condition
Map dataSharpened map of full-length human dynein-1 in phi-like conformation bound to a Lis1 dimer under Nde1-Lis1 condition
Sample
  • Complex: Consensus map of full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition
Keywordsdynein-1 / phi-like conformation / Lis1 / MOTOR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYang J / Zhang K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: Nat Chem Biol / Year: 2025
Title: Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1.
Authors: Jun Yang / Yuanchang Zhao / Pengxin Chai / Ahmet Yildiz / Kai Zhang /
Abstract: Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited ...Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited Phi conformation, a process driven by Lis1 and Nde1/Ndel1. Using biochemical reconstitution and cryo-electron microscopy, we demonstrate that Nde1 enhances Lis1 binding to autoinhibited dynein and facilitates Phi opening. We identify a key intermediate in this activation pathway where a single Lis1 dimer binds between Phi-like (Phi) motor rings. In this 'Phi-Lis1' complex, Lis1 interacts with one motor domain through canonical sites at the AAA+ (adenosine triphosphatases associated with diverse cellular activities) ring and stalk, and with AAA5, AAA6 and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the Phi-Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of Phi-Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening.
History
DepositionNov 26, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48092.png

Downloads & links

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Map

FileDownload / File: emd_48092.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of full-length human dynein-1 in phi-like conformation bound to a Lis1 dimer under Nde1-Lis1 condition
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.22 Å/pix.
x 400 pix.
= 888.84 Å		2.22 Å/pix.
x 400 pix.
= 888.84 Å		2.22 Å/pix.
x 400 pix.
= 888.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2221 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6137592 - 1.6904902
Average (Standard dev.)-0.00019411357 (±0.041972414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 888.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48092_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_48092_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of full-length human dynein-1 in phi-like...

Fileemd_48092_half_map_1.map
AnnotationHalf map of full-length human dynein-1 in phi-like conformation bound to a Lis1 dimer under Nde1-Lis1 condition
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of full-length human dynein-1 in phi-like...

Fileemd_48092_half_map_2.map
AnnotationHalf map of full-length human dynein-1 in phi-like conformation bound to a Lis1 dimer under Nde1-Lis1 condition
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Consensus map of full-length human dynein-1 in phi-like comformat...

EntireName: Consensus map of full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition
Components
  • Complex: Consensus map of full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition

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Supramolecule #1: Consensus map of full-length human dynein-1 in phi-like comformat...

SupramoleculeName: Consensus map of full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.5 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.2
Details: 25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 82022
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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