8G0Q: Kinetochore protein NDC80

Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment. Determined by X-ray diffraction at 3.22 Å resolution. Released 29 Mar 2023.

Method: X-ray diffraction
Resolution: 3.22 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 7,940
Mol. weight: 122.04 kDa
Released: 29 Mar 2023

Explore 8G0Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G0Q contains 40 α-helices and 0 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	122-138	17
α-helix	141-144	4
α-helix	151-155	5
α-helix	159-173	15
α-helix	183-193	11
α-helix	199-201	3
α-helix	204-208	5
α-helix	215-254	40
α-helix	264-291	28
α-helix	298-683	84

Chain B: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	259-267	9
α-helix	1015-1022	8
α-helix	1030-1033	4
α-helix	1041-1052	12
α-helix	1057-1065	9
α-helix	1073-1075	3
α-helix	1079-1099	21
α-helix	1109-1112	4
α-helix	1116-1136	21
α-helix	1137-1139	3
α-helix	1141-1449	56

Chain C: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	122-138	17
α-helix	141-144	4
α-helix	151-155	5
α-helix	159-173	15
α-helix	183-193	11
α-helix	199-201	3
α-helix	205-207	3
α-helix	215-254	40
α-helix	261-291	31
α-helix	298-683	84

Chain D: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	1013-1022	10
α-helix	1030-1033	4
α-helix	1038-1052	15
α-helix	1057-1064	8
α-helix	1078-1080	3
α-helix	1082-1099	18
α-helix	1109-1112	4
α-helix	1116-1137	22
α-helix	1141-1449	56

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore protein NDC80	A, C	protein	287	Saccharomyces cerevisiae	P40460 (AlphaFold model)
DASH complex subunit DAM1,Kinetochore protein NUF2	B, D	protein	233	Saccharomyces cerevisiae	P33895 (AlphaFold model), P53267 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8G0Q_1 Kinetochore protein NDC80 (chains A, C)
SGSSLQQHLSNRDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGF
IIIFKWLYLRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGML
HWMVRTNIKLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDY
FTESYKSFLKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQ
QVIHVIDITSKFKINIQSSLENSENELGNVIEELRNLEFETEHNVTN

Sequence of entity 2 (B, D), FASTA

>8G0Q_2 DASH complex subunit DAM1,Kinetochore protein NUF2 (chains B, D)
MKLRRKSILHTIRNSIASGARISLGSGAARVVNGPVSRNQDVFPILDLQELVICLQSCDF
ALATQENISRPTSDYMVTLYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTL
NVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFIL
QMESLLGQINKLNDEIKQLQKDFEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ

Primary citation

Structure of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface. Zahm, J.A., Jenni, S., Harrison, S.C. Open Biol (2023) 13:220378-220378. DOI 10.1098/rsob.220378 · PubMed

Other PDB entries of the same protein (UniProt P40460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KDF 2.72 Å, Structure of Stu2 Bound to dwarf Ndc80c
5TCS 2.83 Å, Crystal structure of a Dwarf Ndc80 Tetramer
8V10 3.02 Å, Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex
8Q84 3.15 Å, Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex
8QAU 3.54 Å, Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
8V11 3.95 Å, Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex
8Q85 3.97 Å, Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex
5TD8 7.53 Å, Crystal structure of an Extended Dwarf Ndc80 Complex

Browse structure collections

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