7Z8M

The pointed end complex of dynactin bound to BICDR1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of dynein-dynactin on microtubules shows tandem adaptor binding.

Chaaban, S.Carter, A.P.

(2022) Nature 610: 212-216

  • DOI: https://doi.org/10.1038/s41586-022-05186-y
  • Primary Citation of Related Structures:  
    7Z8F, 7Z8G, 7Z8H, 7Z8I, 7Z8J, 7Z8K, 7Z8L, 7Z8M

  • PubMed Abstract: 

    Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor 1-3 . Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour 4-6 . Different coiled-coil adaptors are linked to different cargos 7,8 , and some share motifs known to contact sites on dynein and dynactin 4,9-13 . There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.


  • Organizational Affiliation

    Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 2A [auth M]405Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2QD80 (Sus scrofa)
Explore A0A5G2QD80 
Go to UniProtKB:  A0A5G2QD80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5G2QD80
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BICD family-like cargo adapter 1B [auth X]577Mus musculusMutation(s): 0 
Gene Names: Bicdl1Bicdr1Ccdc64
UniProt & NIH Common Fund Data Resources
Find proteins for A0JNT9 (Mus musculus)
Explore A0JNT9 
Go to UniProtKB:  A0JNT9
IMPC:  MGI:1922915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0JNT9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin 6C [auth U]190Sus scrofaMutation(s): 0 
UniProt
Find proteins for D0G6S1 (Sus scrofa)
Explore D0G6S1 
Go to UniProtKB:  D0G6S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0G6S1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 4D [auth Y]467Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TB62 (Sus scrofa)
Explore A0A4X1TB62 
Go to UniProtKB:  A0A4X1TB62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1TB62
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Arp11E [auth J]417Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LHK5 (Sus scrofa)
Explore I3LHK5 
Go to UniProtKB:  I3LHK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LHK5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ARP1 actin related protein 1 homolog AF [auth G],
I
376Sus scrofaMutation(s): 0 
UniProt
Find proteins for F2Z5G5 (Sus scrofa)
Explore F2Z5G5 
Go to UniProtKB:  F2Z5G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z5G5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1G [auth H]375Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q6QAQ1 (Sus scrofa)
Explore Q6QAQ1 
Go to UniProtKB:  Q6QAQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6QAQ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 5H [auth V]182Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1UWQ6 (Sus scrofa)
Explore A0A4X1UWQ6 
Go to UniProtKB:  A0A4X1UWQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1UWQ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
M [auth J]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
O [auth G],
Q [auth H],
S [auth I]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth Y],
K [auth Y],
L [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth J],
P [auth G],
R [auth H],
T [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210711/Z/18/Z
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A025_1011
European Molecular Biology Organization (EMBO)European UnionALTF 334-2020

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references
  • Version 1.2: 2022-10-19
    Changes: Database references