3IZ0

Human Ndc80 Bonsai Decorated Microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.6 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

The Ndc80 kinetochore complex forms oligomeric arrays along microtubules.

Alushin, G.M.Ramey, V.H.Pasqualato, S.Ball, D.A.Grigorieff, N.Musacchio, A.Nogales, E.

(2010) Nature 467: 805-810

  • DOI: 10.1038/nature09423

  • PubMed Abstract: 
  • The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we present a subnanometre-resolution cryo-electron micro ...

    The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we present a subnanometre-resolution cryo-electron microscopy reconstruction of the human Ndc80 complex bound to microtubules, sufficient for precise docking of crystal structures of the component proteins. We find that the Ndc80 complex binds the microtubule with a tubulin monomer repeat, recognizing α- and β-tubulin at both intra- and inter-tubulin dimer interfaces in a manner that is sensitive to tubulin conformation. Furthermore, Ndc80 complexes self-associate along protofilaments through interactions mediated by the amino-terminal tail of the NDC80 protein, which is the site of phospho-regulation by Aurora B kinase. The complex's mode of interaction with the microtubule and its oligomerization suggest a mechanism by which Aurora B could regulate the stability of load-bearing kinetochore-microtubule attachments.


    Organizational Affiliation

    Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha tubulin, Chain A from PDB 1JFF
A
451Bos taurusN/A
Find proteins for P81947 (Bos taurus)
Go to UniProtKB:  P81947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
beta tubulin, Chain B from PDB 1JFF
B
445Bos taurusGene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Go to Gene View: TUBB2B
Go to UniProtKB:  Q6B856
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai)
C, E
315Homo sapiensGene Names: SPC25 (SPBC25), NDC80 (HEC, HEC1, KNTC2)
Find proteins for Q9HBM1 (Homo sapiens)
Go to Gene View: SPC25
Go to UniProtKB:  Q9HBM1
Find proteins for O14777 (Homo sapiens)
Go to Gene View: NDC80
Go to UniProtKB:  O14777
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NUF2-SPC24 chimera protein, Chain D from PDB 2VE7 (Ndc80 bonsai)
D, F
250Homo sapiensGene Names: SPC24 (SPBC24), NUF2 (CDCA1, NUF2R)
Find proteins for Q8NBT2 (Homo sapiens)
Go to Gene View: SPC24
Go to UniProtKB:  Q8NBT2
Find proteins for Q9BZD4 (Homo sapiens)
Go to Gene View: NUF2
Go to UniProtKB:  Q9BZD4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TA1
Query on TA1

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Download CCD File 
B
TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.6 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-19
    Type: Database references