6RZB

Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule.

Lacey, S.E.He, S.Scheres, S.H.Carter, A.P.

(2019) Elife 8

  • DOI: 10.7554/eLife.47145
  • Primary Citation of Related Structures:  
    6RZA, 6RZB

  • PubMed Abstract: 
  • Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address ...

    Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB426Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MKIAA0325 proteinC149Mus musculusMutation(s): 2 
Gene Names: Dync1h1Dnchc1mKIAA0325Dhc1Dnch1Dyhc
Find proteins for Q9JHU4 (Mus musculus)
Explore Q9JHU4 
Go to UniProtKB:  Q9JHU4
NIH Common Fund Data Resources
IMPC  MGI:103147
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA437Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download CCD File 
B
TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
 Ligand Interaction
GTP
Query on GTP

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A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011
Wellcome TrustUnited KingdomWT210711

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references