7KZM

Outer dynein arm bound to doublet microtubules from C. reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a microtubule-bound axonemal dynein.

Walton, T.Wu, H.Brown, A.

(2021) Nat Commun 12: 477-477

  • DOI: https://doi.org/10.1038/s41467-020-20735-7
  • Primary Citation of Related Structures:  
    7KZM, 7KZN, 7KZO

  • PubMed Abstract: 

    Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta443Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha451Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain alphaO [auth A]4,503Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellar outer dynein arm heavy chain betaP [auth B]4,568Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein gamma chain, flagellar outer armQ [auth C]4,485Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein, 78 kDa intermediate chain, flagellar outer armR [auth D]683Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein, 70 kDa intermediate chain, flagellar outer armS [auth E]567Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellar outer dynein arm light chain 2T [auth F]136Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein 18 kDa light chain, flagellar outer armU [auth G]159Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein 11 kDa light chain, flagellar outer armV [auth H]120Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock LC7aW [auth I]105Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock LC7bX [auth J]100Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein 8 kDa light chain, flagellar outer armAA [auth M],
BA [auth N],
Y [auth K],
Z [auth L]
91Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 9CA [auth O]117Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 10DA [auth P]103Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm-docking complex subunit 1EA [auth X],
GA [auth X1]
749Chlamydomonas reinhardtiiMutation(s): 0 
EC: 2.7.1
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DC1FA [auth X0]162Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm protein 1HA [auth Y],
JA [auth Y1]
552Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DC2IA [auth Y0]168Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm-docking complex protein DC3KA [auth Z]184Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
CB [auth B5]
FB [auth B7]
LA [auth A1]
PA [auth A3]
SA [auth A5]
CB [auth B5],
FB [auth B7],
LA [auth A1],
PA [auth A3],
SA [auth A5],
VA [auth A7],
YA [auth B2]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
AB [auth B3]
DB [auth B5]
GB [auth B7]
NA [auth A1]
QA [auth A3]
AB [auth B3],
DB [auth B5],
GB [auth B7],
NA [auth A1],
QA [auth A3],
TA [auth A5],
WA [auth A7],
XA [auth B1]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth B4]
EB [auth B6]
MA [auth A1]
OA [auth A2]
RA [auth A4]
BB [auth B4],
EB [auth B6],
MA [auth A1],
OA [auth A2],
RA [auth A4],
UA [auth A6],
ZA [auth B3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references