8QAU

Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex

• PDB DOI: https://doi.org/10.2210/pdb8QAU/pdb
• EM Map EMD-18304: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Sus scrofa, Saccharomyces cerevisiae
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-08-23 Released: 2024-04-03 
• Deposition Author(s): Muir, K.W., Barford, D.
• Funding Organization(s): UK Research and Innovation (UKRI), Cancer Research UK

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction

Muir, K.W., Batters, C., Dendooven, T., Yang, J., Zhang, Z., Burt, A., Barford, D.

(2023) Biorxiv 

• DOI: https://doi.org/10.1101/2023.07.20.549907

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 273.99 kDa 
• Atom Count: 10,137 
• Modelled Residue Count: 1,347 
• Deposited Residue Count: 2,381 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A [auth C]	451	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02550 (Sus scrofa) Explore P02550  Go to UniProtKB:  P02550

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B [auth D]	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554  Go to UniProtKB:  P02554

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinetochore protein NDC80	C [auth A]	691	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: NDC80
UniProt
Find proteins for P40460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40460  Go to UniProtKB:  P40460

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinetochore protein NUF2	D [auth B]	451	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: NUF2
UniProt
Find proteins for P33895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33895  Go to UniProtKB:  P33895

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DASH complex subunit DAM1	E	343	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: DAM1
UniProt
Find proteins for P53267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53267  Go to UniProtKB:  P53267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TA1	I [auth D]	TAXOL C47 H51 N O14 RCINICONZNJXQF-MZXODVADSA-N
GTP	F [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	H [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Muir, K.W., Barford, D.

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Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	MC_UP_1201/6
Cancer Research UK	United Kingdom	C576/A14109

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release