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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
SampleComplete human cytoplasmic dynein-1 in the phi-particle conformation
SourceHomo sapiens / human
Map datacomplete human cytoplasmic dynein-1
Methodsingle particle reconstruction, at 15 Å resolution
AuthorsZhang K
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: 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
3D viewer


View / / Stereo:
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Orientation
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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 package.

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 / arthropod

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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

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 / 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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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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