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


This is version 1.0 of the entry. See complete history. 


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 break in helical symmetry known as the seam ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neuronal migration protein doublecortinA [auth N]99Homo sapiensMutation(s): 0 
Gene Names: DCX, DBCN, LISX
UniProt & NIH Common Fund Data Resources
Find proteins for O43602 (Homo sapiens)
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Go to UniProtKB:  O43602
PHAROS:  O43602
GTEx:  ENSG00000077279 
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UniProt GroupO43602
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-2B chainD [auth B],
B [auth b]		429Bos taurusMutation(s): 0 
Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus)
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Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainC [auth A],
E [auth a]		432Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
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Go to UniProtKB:  P81947
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UniProt GroupP81947
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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G [auth A],
J [auth a]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
F [auth b],
I [auth B]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
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H [auth A],
K [auth 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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View more in-depth experimental data

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  (Full details and data files)

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