Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131.06 kDa 
• Atom Count: 8258 
• Modelled Residue Count: 1010 
• Deposited Residue Count: 1130 
• Unique protein chains: 2

2VE7

Crystal structure of a bonsai version of the human Ndc80 complex

• DOI: 10.2210/pdb2VE7/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-10-17 Released: 2008-05-13 
• Deposition Author(s): Ciferri, C., Pasqualato, S., Dos Reis, G., Screpanti, E., Maiolica, A., Polka, J., De Luca, J.G., De Wulf, P., Salek, M., Rappsilber, J., Moores, C.A., Salmon, E.D., Musacchio, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.261 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Implications for Kinetochore-Microtubule Attachment from the Structure of an Engineered Ndc80 Complex

Ciferri, C., Pasqualato, S., Screpanti, E., Varetti, G., Santaguida, S., Dos Reis, G., Maiolica, A., Polka, J., De Luca, J.G., De Wulf, P., Salek, M., Rappsilber, J., Moores, C.A., Salmon, E.D., Musacchio, A.

(2008) Cell 133: 427

• PubMed: 18455984 
• DOI: 10.1016/j.cell.2008.03.020
• Primary Citation of Related Structures:  
  2VE7


• PubMed Abstract: 
  

Kinetochores are proteinaceous assemblies that mediate the interaction of chromosomes with the mitotic spindle. The 180 kDa Ndc80 complex is a direct point of contact between kinetochores and microtubules. Its four subunits contain coiled coils and form an elongated rod structure with functional globular domains at either end. We crystallized an engineered "bonsai" Ndc80 complex containing a shortened rod domain but retaining the globular domains required for kinetochore localization and microtubule binding. The structure reveals a microtubule-binding interface containing a pair of tightly interacting calponin-homology (CH) domains with a previously unknown arrangement. The interaction with microtubules is cooperative and predominantly electrostatic. It involves positive charges in the CH domains and in the N-terminal tail of the Ndc80 subunit and negative charges in tubulin C-terminal tails and is regulated by the Aurora B kinase. We discuss our results with reference to current models of kinetochore-microtubule attachment and centromere organization.

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Organizational Affiliation: 

Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, I 20139 Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25	A, B	315	Homo sapiens	Mutation(s): 0  Gene Names: NDC80, HEC, HEC1, KNTC2, SPC25, SPBC25, AD024
Find proteins for Q9HBM1 (Homo sapiens) Explore Q9HBM1  Go to UniProtKB:  Q9HBM1
NIH Common Fund Data Resources
PHAROS:  Q9HBM1 GTEx:  ENSG00000152253
Find proteins for O14777 (Homo sapiens) Explore O14777  Go to UniProtKB:  O14777
NIH Common Fund Data Resources
PHAROS:  O14777 GTEx:  ENSG00000080986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24	C, D	250	Homo sapiens	Mutation(s): 1  Gene Names: SPC24, SPBC24, NUF2, CDCA1, NUF2R
Find proteins for Q9BZD4 (Homo sapiens) Explore Q9BZD4  Go to UniProtKB:  Q9BZD4
NIH Common Fund Data Resources
PHAROS:  Q9BZD4 GTEx:  ENSG00000143228
Find proteins for Q8NBT2 (Homo sapiens) Explore Q8NBT2  Go to UniProtKB:  Q8NBT2
NIH Common Fund Data Resources
PHAROS:  Q8NBT2 GTEx:  ENSG00000161888

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	C, D	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.261 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.653	α = 90
b = 248.965	β = 90
c = 58.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
pirate	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-10-17 
• Released Date: 2008-05-13 
Deposition Author(s): Ciferri, C., Pasqualato, S., Dos Reis, G., Screpanti, E., Maiolica, A., Polka, J., De Luca, J.G., De Wulf, P., Salek, M., Rappsilber, J., Moores, C.A., Salmon, E.D., Musacchio, A.

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2017-06-21
  Changes: Refinement description