8V10: Saccharomyces cerevisiae Mps1 peptide

Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex. Determined by X-ray diffraction at 3.02 Å resolution. Released 15 May 2024.

Method: X-ray diffraction
Resolution: 3.02 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 5,725
Mol. weight: 85.39 kDa
Ligands: NI
Released: 15 May 2024

Explore 8V10 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V10 contains 29 α-helices and 7 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	122-138	17
α-helix	141-145	5
α-helix	151-155	5
α-helix	159-173	15
α-helix	184-193	10
α-helix	204-207	4
α-helix	215-245	31
α-helix	250-254	5
α-helix	257-258	2
α-helix	261-291	31
α-helix	298-680	81

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	166-168	3
α-helix	1013-1022	10
α-helix	1031-1034	4
α-helix	1038-1048	11
α-helix	1049-1053	5
α-helix	1057-1064	8
α-helix	1075-1101	27
α-helix	1109-1112	4
α-helix	1116-1136	21
α-helix	1141-1449	56

Chain C: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	25-53	29
β-strand	57-60	4	1
β-strand	65-69	5	1
β-strand	76-80	5	1
α-helix	87-94	8

Chain D: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-24	18
α-helix	32-38	7
β-strand	41-45	5	2
β-strand	53-57	5	2
β-strand	63-67	5	2
β-strand	75-78	4	2
α-helix	84-95	12
α-helix	100-113	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore protein NDC80	A	protein	279	Saccharomyces cerevisiae	P40460 (AlphaFold model)
Mps1/NUF2 chimera protein	B	protein	233	Saccharomyces cerevisiae	P33895 (AlphaFold model), P54199 (AlphaFold model)
Kinetochore protein SPC24	C	protein	100	Saccharomyces cerevisiae	Q04477 (AlphaFold model)
Kinetochore protein SPC25	D	protein	115	Saccharomyces cerevisiae	P40014

Sequence of entity 1 (A), FASTA

>8V10_1 Kinetochore protein NDC80 (chains A)
SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLY
LRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNI
KLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSF
LKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDI
TSKFKINIQSSLENSENELGNVIEELRNLEFETEHNVTN

Sequence of entity 2 (B), FASTA

>8V10_2 Mps1/NUF2 chimera protein (chains B)
MRQNMKEDITAKYAERRSKRFLISNRTTKLGPAKRASRNQDVFPILDLQELVICLQSCDF
ALATQENISRPTSDYMVTLYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTL
NVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFIL
QMESLLGQINKLNDEIKQLQKDFEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ

Sequence of entity 3 (C), FASTA

>8V10_3 Kinetochore protein SPC24 (chains C)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARLKLYRSLGVILD
LENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Sequence of entity 4 (D), FASTA

>8V10_4 Kinetochore protein SPC25 (chains D)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHVALYERLLQLRVLPGASDVHDVRFVFGDD
SRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1

Primary citation

A communication hub for phosphoregulation of kinetochore-microtubule attachment. Zahm, J.A., Harrison, S.C. Curr Biol (2024) 34:2308-2318.e6. DOI 10.1016/j.cub.2024.04.067 · 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
8Q84 3.15 Å, Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex
8G0Q 3.22 Å, Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment
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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