6RF8

Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

A microtubule RELION-based pipeline for cryo-EM image processing.

Cook, A.D., Manka, S.W., Wang, S., Moores, C.A., Atherton, J.

(2020) J Struct Biol 209: 107402-107402

  • DOI: 10.1016/j.jsb.2019.10.004
  • Primary Citation of Related Structures:  
    6RF8

  • PubMed Abstract: 

    • Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a ...

    Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.

    Organizational Affiliation: 

    Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, United Kingdom. Electronic address: j.atherton@mail.cryst.bbk.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neuronal migration protein doublecortin N99Homo sapiensMutation(s): 0 
Gene Names: DCX, DBCN, LISX
Find proteins for O43602 (Homo sapiens)
Explore O43602 
Go to UniProtKB:  O43602
NIH Common Fund Data Resources
PHAROS:  O43602
GTEx:  ENSG00000077279
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-2B chain B, b429Bos taurusMutation(s): 0 
Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chain A, a432Bos taurusMutation(s): 0 
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
A, a
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
B, b
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, a
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-12 
  • Released Date: 2020-04-15 
    • Deposition Author(s): Manka, S.W.
Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/R000352/1

Revision History 

  • Version 1.0: 2020-04-15
    Type: Initial release