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- EMDB-3705: Full length human cytoplasmic dynein-1 in the phi-particle confor... -

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Basic information

Entry
Database: EMDB / ID: 3705
TitleFull length human cytoplasmic dynein-1 in the phi-particle conformation
Map datacomplete human cytoplasmic dynein-1
SampleComplete human cytoplasmic dynein-1 in the phi-particle conformation
  • Dynein motor domain
  • (Dynein tail heavy ...) x 2
  • Dynein intermediate chain
  • (Dynein light intermediate ...) x 2
  • (N-terminal dimerization ...) x 2
  • LC8
  • (Tctex) x 2
  • (Intermediate chain N-terminus ...) x 2
  • Robl
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 15 Å resolution
AuthorsZhang K
CitationJournal: Cell / Year: 2017
Title: Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Authors: Kai Zhang / Helen E Foster / Arnaud Rondelet / Samuel E Lacey / Nadia Bahi-Buisson / Alexander W Bird / Andrew P Carter
Abstract: Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves ...Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity.
Validation ReportPDB-ID: 5nvu

SummaryFull reportAbout validation report
DateDeposition: May 4, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Sep 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5nvu
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3705.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
2.64 Å/pix.
= 792. Å
300 pix
2.64 Å/pix.
= 792. Å
300 pix
2.64 Å/pix.
= 792. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.64 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.2635953 - 0.43869567
Average (Standard dev.)0.00020694571 (0.0106563335)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
CellA=B=C: 792.00006 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.642.642.64
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z792.000792.000792.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-0.2640.4390.000

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Supplemental data

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Sample components

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Entire Complete human cytoplasmic dynein-1 in the phi-particle conformation

EntireName: Complete human cytoplasmic dynein-1 in the phi-particle conformation
Number of components: 15

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Component #1: protein, Complete human cytoplasmic dynein-1 in the phi-particle ...

ProteinName: Complete human cytoplasmic dynein-1 in the phi-particle conformation
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Dynein motor domain

ProteinName: Dynein motor domain / Recombinant expression: No
MassTheoretical: 269.723031 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Dynein tail heavy chain

ProteinName: Dynein tail heavy chain / Recombinant expression: No
MassTheoretical: 79.335086 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Dynein intermediate chain

ProteinName: Dynein intermediate chain / Recombinant expression: No
MassTheoretical: 29.804609 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Dynein tail heavy chain

ProteinName: Dynein tail heavy chain / Recombinant expression: No
MassTheoretical: 76.016109 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Dynein light intermediate chain

ProteinName: Dynein light intermediate chain / Recombinant expression: No
MassTheoretical: 25.379143 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Dynein light intermediate chain

ProteinName: Dynein light intermediate chain / Recombinant expression: No
MassTheoretical: 25.12383 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, N-terminal dimerization domain

ProteinName: N-terminal dimerization domain / Recombinant expression: No
MassTheoretical: 10.656127 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, N-terminal dimerization domain

ProteinName: N-terminal dimerization domain / Recombinant expression: No
MassTheoretical: 10.571022 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, LC8

ProteinName: LC8 / Recombinant expression: No
MassTheoretical: 7.25193 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, Tctex

ProteinName: Tctex / Recombinant expression: No
MassTheoretical: 8.783818 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, Tctex

ProteinName: Tctex / Recombinant expression: No
MassTheoretical: 8.868924 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, Intermediate chain N-terminus peptides

ProteinName: Intermediate chain N-terminus peptides / Recombinant expression: No
MassTheoretical: 2.315846 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: protein, Intermediate chain N-terminus peptides

ProteinName: Intermediate chain N-terminus peptides / Recombinant expression: No
MassTheoretical: 2.486056 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #15: protein, Robl

ProteinName: Robl / Recombinant expression: No
MassTheoretical: 10.230603 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 28736
3D reconstructionSoftware: RELION / Resolution: 15 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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