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

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Entry
Database: EMDB / ID: 3706
TitleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Map data3D reconstruction of DDB. Motor domains has The stable portion of the dynein tail is visible, whereas the motor domains are disordered.
SampleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
  • dynein-1
  • dynactin
  • BICD2
  • (dynein heavy ...) x 2
  • (dynein intermediate ...) x 2
  • (dynein N-terminal dimerization ...) x 2
  • Robl
  • (dynein light intermediate ...) x 2
  • Arp1
  • beta-actin
  • Arp11
  • Capping protein (Actin filament) muscle Z-line, alpha 1
  • F-actin capping protein beta subunit variant II
  • (dynactin shoulder ...) x 4
  • Dynactin 6
  • Dynactin subunit 5
  • dynactin pointed end p62
  • p150
  • (Dynactin) x 4
  • dynactin p150
  • BICD2N
Function / homologyActin / F-actin capping protein alpha subunit / Actins and actin-related proteins signature. / F-actin capping protein alpha subunit signature 2. / F-actin capping protein alpha subunit signature 1. / Actins signature 2. / Actins signature 1. / F-actin capping protein beta subunit signature. / Dynamitin / F-actin capping protein, beta subunit ...Actin / F-actin capping protein alpha subunit / Actins and actin-related proteins signature. / F-actin capping protein alpha subunit signature 2. / F-actin capping protein alpha subunit signature 1. / Actins signature 2. / Actins signature 1. / F-actin capping protein beta subunit signature. / Dynamitin / F-actin capping protein, beta subunit / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Bacterial transferase hexapeptide (six repeats) / F-actin-capping protein subunit alpha/beta / Actin-related protein 1 family / Dynamitin / Dynactin subunit 6 / Actin-related protein 10 / Actin/actin-like conserved site / F-actin capping protein, beta subunit, conserved site / MHC class II antigen presentation / COPI-mediated anterograde transport / Trimeric LpxA-like superfamily / Adherens junctions interactions / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / Anchoring of the basal body to the plasma membrane / Cell-extracellular matrix interactions / Interaction between L1 and Ankyrins / VEGFA-VEGFR2 Pathway / Recycling pathway of L1 / EPHB-mediated forward signaling / COPI-independent Golgi-to-ER retrograde traffic / Recruitment of NuMA to mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Regulation of actin dynamics for phagocytic cup formation / Formation of annular gap junctions / Gap junction degradation / F-actin capping protein, alpha subunit, conserved site / Actin, conserved site / MAP2K and MAPK activation / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / Clathrin-mediated endocytosis / AURKA Activation by TPX2 / Advanced glycosylation endproduct receptor signaling / COPI-independent Golgi-to-ER retrograde traffic / Actin family / RHO GTPases Activate Formins / Neutrophil degranulation / Hexapeptide repeat / F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha / WASH complex / dynactin complex / F-actin capping protein complex / dense body / profilin binding / coronary vasculature development / aorta development / cell cortex region / barbed-end actin filament capping / ventricular septum development / cell junction assembly / sarcomere organization / myofibril / condensed chromosome kinetochore / filamentous actin / microtubule-based process / phagocytic vesicle / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule-based movement / cellular response to interferon-gamma / structural constituent of cytoskeleton / actin cytoskeleton organization / actin binding / ER to Golgi vesicle-mediated transport / nuclear membrane / cytoskeleton / centrosome / myelin sheath / ubiquitin protein ligase binding / focal adhesion / nucleotide binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm / F-actin capping protein beta subunit variant II / Actin gamma 1 / Actin related protein 10 homolog / ARP1 actin related protein 1 homolog A / Dynactin / Dynactin 6 / Capping protein (Actin filament) muscle Z-line, alpha 1
Function and homology information
SourceHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / 8.7 Å resolution
AuthorsZhang K / Foster HE
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: 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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5nw4
  • 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_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.

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 (fall armyworm)

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Component #3: protein, dynactin

ProteinName: dynactin / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #4: protein, BICD2

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

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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 (pig)

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Component #15: protein, beta-actin

ProteinName: beta-actin / Recombinant expression: No
MassTheoretical: 43.987133 kDa
SourceSpecies: Sus scrofa (pig)

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Component #16: protein, Arp11

ProteinName: Arp11 / Recombinant expression: No
MassTheoretical: 46.250785 kDa
SourceSpecies: Sus scrofa (pig)

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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 (pig)

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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 (pig)

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Component #19: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 48.613012 kDa
SourceSpecies: Sus scrofa (pig)

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Component #20: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 51.251293 kDa
SourceSpecies: Sus scrofa (pig)

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Component #21: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 11.081651 kDa
SourceSpecies: Sus scrofa (pig)

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Component #22: protein, dynactin shoulder complex

ProteinName: dynactin shoulder complex / Recombinant expression: No
MassTheoretical: 14.826253 kDa
SourceSpecies: Sus scrofa (pig)

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Component #23: protein, Dynactin 6

ProteinName: Dynactin 6 / Recombinant expression: No
MassTheoretical: 20.70391 kDa
SourceSpecies: Sus scrofa (pig)

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Component #24: protein, Dynactin subunit 5

ProteinName: Dynactin subunit 5 / Recombinant expression: No
MassTheoretical: 24.538305 kDa
SourceSpecies: Sus scrofa (pig)

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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 (pig)

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Component #26: protein, p150

ProteinName: p150 / Recombinant expression: No
MassTheoretical: 4.443468 kDa
SourceSpecies: Sus scrofa (pig)

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Component #27: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 5.400015 kDa
SourceSpecies: Sus scrofa (pig)

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Component #28: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 7.931814 kDa
SourceSpecies: Sus scrofa (pig)

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Component #29: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 3.019344 kDa
SourceSpecies: Sus scrofa (pig)

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Component #30: protein, Dynactin

ProteinName: Dynactin / Recombinant expression: No
MassTheoretical: 2.237488 kDa
SourceSpecies: Sus scrofa (pig)

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Component #31: protein, dynactin p150

ProteinName: dynactin p150 / Recombinant expression: No
MassTheoretical: 4.528573 kDa
SourceSpecies: Sus scrofa (pig)

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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

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

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Atomic model buiding

Output model

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