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- EMDB-3706: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co... -

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Basic information

Entry
Database: EMDB / ID: 3706
TitleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
SampleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
SourceHomo sapiens / human
Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
Map data3D reconstruction of DDB. Motor domains has The stable portion of the dynein tail is visible, whereas the motor domains are disordered.
Methodsingle particle reconstruction, at 8.7 Å resolution
AuthorsZhang K / Foster HE
CitationCell, 2017, 169, 1303-1314.e18

Cell, 2017, 169, 1303-1314.e18 Yorodumi Papers
Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Kai Zhang / Helen E Foster / Arnaud Rondelet / Samuel E Lacey / Nadia Bahi-Buisson / Alexander W Bird / Andrew P Carter

Validation ReportPDB-ID: 5nw4

SummaryFull reportAbout validation report
DateDeposition: May 5, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Sep 13, 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
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  • Surface view with fitted model
  • Atomic models: : PDB-5nw4
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3706.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
2.68 Å/pix.
= 964.8 Å
360 pix
2.68 Å/pix.
= 964.8 Å
360 pix
2.68 Å/pix.
= 964.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.68 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.20258602 - 0.47286594
Average (Standard dev.)0.00025378444 (0.0064759557)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 964.80005 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.682.682.68
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z964.800964.800964.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2030.4730.000

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Supplemental data

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Sample components

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Entire Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co...

EntireName: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Number of components: 32
MassTheoretical: 2.5 MDa

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Component #1: protein, Human cytoplasmic dynein-1 bound to dynactin and an N-te...

ProteinName: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Recombinant expression: No
MassTheoretical: 2.5 MDa

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Component #2: protein, dynein-1

ProteinName: dynein-1 / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #3: protein, dynactin

ProteinName: dynactin / Recombinant expression: No
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #4: protein, BICD2

ProteinName: BICD2 / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #5: protein, dynein heavy chain

ProteinName: dynein heavy chain / Recombinant expression: No
MassTheoretical: 75.675695 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #6: protein, dynein intermediate chain

ProteinName: dynein intermediate chain / Recombinant expression: No
MassTheoretical: 29.038656 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #7: 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 #8: protein, dynein heavy chain

ProteinName: dynein heavy chain / Recombinant expression: No
MassTheoretical: 78.484062 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #9: protein, dynein N-terminal dimerization domain

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

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Component #10: protein, dynein N-terminal dimerization domain

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

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Component #11: protein, Robl

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

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Component #12: 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 #13: 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 #14: protein, Arp1

ProteinName: Arp1 / Recombinant expression: No
MassTheoretical: 42.684711 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #15: protein, beta-actin

ProteinName: beta-actin / Recombinant expression: No
MassTheoretical: 43.987133 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #16: protein, Arp11

ProteinName: Arp11 / Recombinant expression: No
MassTheoretical: 46.250785 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #17: protein, Capping protein (Actin filament) muscle Z-line, alpha 1

ProteinName: Capping protein (Actin filament) muscle Z-line, alpha 1
Recombinant expression: No
MassTheoretical: 33.059848 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #18: protein, F-actin capping protein beta subunit variant II

ProteinName: F-actin capping protein beta subunit variant II / Recombinant expression: No
MassTheoretical: 33.060379 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #19: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 48.613012 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #20: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 51.251293 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #21: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 11.081651 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #22: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 14.826253 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #23: protein, Dynactin 6

ProteinName: Dynactin 6 / Recombinant expression: No
MassTheoretical: 20.70391 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #24: protein, Dynactin subunit 5

ProteinName: Dynactin subunit 5 / Recombinant expression: No
MassTheoretical: 24.538305 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #25: protein, dynactin pointed end p62

ProteinName: dynactin pointed end p62 / Recombinant expression: No
MassTheoretical: 20.698426 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #26: protein, p150

ProteinName: p150 / Recombinant expression: No
MassTheoretical: 4.443468 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #27: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 5.400015 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #28: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 7.931814 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #29: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 3.019344 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #30: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 2.237488 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #31: protein, dynactin p150

ProteinName: dynactin p150 / Recombinant expression: No
MassTheoretical: 4.528573 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #32: protein, BICD2N

ProteinName: BICD2N / Recombinant expression: No
MassTheoretical: 23.421752 kDa
Source (engineered)Expression System: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
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 / Number of projections: 78671
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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