5OWO

Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM shows how dynactin recruits two dyneins for faster movement.

Urnavicius, L.Lau, C.K.Elshenawy, M.M.Morales-Rios, E.Motz, C.Yildiz, A.Carter, A.P.

(2018) Nature 554: 202-206

  • DOI: 10.1038/nature25462
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule ...

    Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine.


    Organizational Affiliation

    Department of Biochemistry, CINVESTAV, México D.F., Mexico.,Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge CB2 0QH, UK.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.,Physics Department, University of California at Berkeley, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic dynein 1 heavy chain 1
A, B, C, D
201Homo sapiensMutation(s): 0 
Gene Names: DYNC1H1 (DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325)
Find proteins for Q14204 (Homo sapiens)
Go to Gene View: DYNC1H1
Go to UniProtKB:  Q14204
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.242α = 90.00
b = 175.560β = 90.00
c = 50.444γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
AutoSolphasing
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT100387
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011
National Institutes of HealthUnited StatesGM094522
NSFUnited StatesMCB-1055017
NSFUnited StatesMCB- 1617028

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection
  • Version 1.2: 2019-10-16
    Type: Data collection