6F38

Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
ARP1 actin related protein 1 homolog A
A, B, C, D, E, F, G, I
376Sus scrofaMutation(s): 0 
Gene Names: ACTR1A
Find proteins for F2Z5G5 (Sus scrofa)
Go to Gene View: ACTR1A
Go to UniProtKB:  F2Z5G5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin, cytoplasmic 1
H
375Sus scrofaMutation(s): 0 
Gene Names: ACTB
Find proteins for Q6QAQ1 (Sus scrofa)
Go to Gene View: ACTB
Go to UniProtKB:  Q6QAQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin related protein 10 homolog
J
390Sus scrofaMutation(s): 0 
Gene Names: ACTR10
Find proteins for I3LHK5 (Sus scrofa)
Go to Gene View: ACTR10
Go to UniProtKB:  I3LHK5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capping protein (Actin filament) muscle Z-line, alpha 1
K
286Sus scrofaMutation(s): 0 
Gene Names: CP alpha1 (Capza, CAPZA1)
Find proteins for A0PFK5 (Sus scrofa)
Go to UniProtKB:  A0PFK5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
F-actin capping protein beta subunit
L
272Sus scrofaMutation(s): 0 
Gene Names: Capzb (CAPZB)
Find proteins for A9XFX6 (Sus scrofa)
Go to UniProtKB:  A9XFX6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 2
M
587N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 2
N
616N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 3
O, P
65N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 2
Q, R
87N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Dynactin 6
U
190Sus scrofaMutation(s): 0 
Gene Names: DCTN6
Find proteins for D0G6S1 (Sus scrofa)
Go to Gene View: DCTN6
Go to UniProtKB:  D0G6S1
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Dynactin subunit 5
V
182Sus scrofaMutation(s): 0 
Gene Names: DCTN5
Find proteins for A0A286ZK88 (Sus scrofa)
Go to Gene View: DCTN5
Go to UniProtKB:  A0A286ZK88
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
HOOK3
X, x
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 4
Y
264N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 1
Z
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Dynactin subunit 2
a
68Sus scrofaMutation(s): 0 
Gene Names: DCTN2
Find proteins for F1SKF9 (Sus scrofa)
Go to Gene View: DCTN2
Go to UniProtKB:  F1SKF9
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Dynactin subunit 2
b
90Sus scrofaMutation(s): 0 
Gene Names: DCTN2
Find proteins for F1SKF9 (Sus scrofa)
Go to Gene View: DCTN2
Go to UniProtKB:  F1SKF9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Dynactin subunit 2
c
50Sus scrofaMutation(s): 0 
Gene Names: DCTN2
Find proteins for F1SL58 (Sus scrofa)
Go to Gene View: DCTN2
Go to UniProtKB:  F1SL58
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Dynactin subunit 2
d
29Sus scrofaMutation(s): 0 
Gene Names: DCTN2
Find proteins for F1SKF9 (Sus scrofa)
Go to Gene View: DCTN2
Go to UniProtKB:  F1SKF9
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic dynein 1 heavy chain 1
e, f, m, n
1455Homo 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
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic dynein 1 intermediate chain 2
g, h, o, p
612Homo sapiensMutation(s): 0 
Gene Names: DYNC1I2 (DNCI2, DNCIC2)
Find proteins for Q13409 (Homo sapiens)
Go to Gene View: DYNC1I2
Go to UniProtKB:  Q13409
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic dynein 1 light intermediate chain 2
i, j, q, r
492Homo sapiensMutation(s): 0 
Gene Names: DYNC1LI2 (DNCLI2, LIC2)
Find proteins for O43237 (Homo sapiens)
Go to Gene View: DYNC1LI2
Go to UniProtKB:  O43237
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Dynein light chain roadblock-type 1
k, l, s, t
96Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1 (BITH, DNCL2A, DNLC2A, ROBLD1)
Find proteins for Q9NP97 (Homo sapiens)
Go to Gene View: DYNLRB1
Go to UniProtKB:  Q9NP97
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Dynactin Subunit 1
z
53N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
H
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, I, J
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
M, N, O, P, Q, R, X, x, Y, Z, z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011
Wellcome TrustUnited KingdomWT100387

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Database references
  • Version 1.2: 2018-02-21
    Type: Database references
  • Version 1.3: 2019-10-09
    Type: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2019-12-11
    Type: Other