3IZ0

Human Ndc80 Bonsai Decorated Microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/nature09423
  • Primary Citation of Related Structures:  
    3IZ0

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha tubulin, Chain A from PDB 1JFF451Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
beta tubulin, Chain B from PDB 1JFF445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B856
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai)
C, E
315Homo sapiensMutation(s): 0 
Gene Names: NDC80 SPC25SPBC25AD024
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBM1 (Homo sapiens)
Explore Q9HBM1 
Go to UniProtKB:  Q9HBM1
PHAROS:  Q9HBM1
GTEx:  ENSG00000152253 
Find proteins for O14777 (Homo sapiens)
Explore O14777 
Go to UniProtKB:  O14777
PHAROS:  O14777
GTEx:  ENSG00000080986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9HBM1O14777
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NUF2-SPC24 chimera protein, Chain D from PDB 2VE7 (Ndc80 bonsai)
D, F
250Homo sapiensMutation(s): 1 
Gene Names: NUF2RP11-77M5.2-004SPC24
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBT2 (Homo sapiens)
Explore Q8NBT2 
Go to UniProtKB:  Q8NBT2
PHAROS:  Q8NBT2
GTEx:  ENSG00000161888 
Find proteins for Q9BZD4 (Homo sapiens)
Explore Q9BZD4 
Go to UniProtKB:  Q9BZD4
PHAROS:  Q9BZD4
GTEx:  ENSG00000143228 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8NBT2Q9BZD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download Ideal Coordinates CCD File 
K [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
I [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
J [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TA1 BindingDB:  3IZ0 EC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description