8QAU | pdb_00008qau

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

Experimental Data Snapshot

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

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A [auth C]	451	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P02550 (Sus scrofa) Explore P02550 Go to UniProtKB: P02550
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02550
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40460
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33895
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53267
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TA1 Query on TA1 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Muir, K.W.

Barford, D.

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 (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release
Version 1.1: 2025-10-01
Changes: Advisory, Data collection, Derived calculations, Structure summary