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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
SourceSus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
Alligator mississippiensis / reptile
Homo sapiens / human
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 StrPapers
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: Aug 2, 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-5nw4
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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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: 29
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 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 #3: 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 #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 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 #6: 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 #7: 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 #8: protein, Robl

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

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Component #9: 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 #10: 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 #11: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / 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 #12: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 43.987133 kDa
SourceSpecies: Alligator mississippiensis / reptile

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Component #13: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / 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 #14: 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 #15: 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 #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: protein, Dynactin subunit 5

ProteinName: Dynactin subunit 5 / Recombinant expression: No
MassTheoretical: 24.538305 kDa
SourceSpecies: Homo sapiens / human

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Component #22: 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 #23: 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 #24: 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 #25: 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 #26: 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 #27: 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 #28: 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 #29: 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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