5TCS: Dwarf Ndc80 Tetramer

Crystal structure of a Dwarf Ndc80 Tetramer. Determined by X-ray diffraction at 2.83 Å resolution. Released 23 Nov 2016.

Method: X-ray diffraction
Resolution: 2.83 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 5,708
Mol. weight: 83.7 kDa
Ligands: MG
Released: 23 Nov 2016

Explore 5TCS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TCS contains 26 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	122-138	17
α-helix	141-144	4
α-helix	159-173	15
α-helix	184-194	11
α-helix	199-201	3
α-helix	204-207	4
α-helix	215-254	40
α-helix	257-260	4
α-helix	267-292	26
α-helix	298-679	80

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	-9--6	4
α-helix	13-22	10
α-helix	40-52	13
α-helix	57-64	8
α-helix	79-100	22
α-helix	109-112	4
α-helix	116-447	79

Chain C: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	24-168	32
β-strand	170-173	4	1
β-strand	178-181	4	1
β-strand	190-193	4	1
α-helix	200-209	10

Chain D: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-24	18
α-helix	31-145	9
β-strand	147-154	8	2
β-strand	157-163	7	2
β-strand	169-173	5	2
β-strand	181-184	4	2
α-helix	190-198	9
α-helix	199-203	5
α-helix	206-219	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore protein NDC80	A	protein	277	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40460 (AlphaFold model)
Kinetochore protein NUF2	B	protein	215	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33895 (AlphaFold model)
Kinetochore protein SPC24	C	protein	100	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q04477 (AlphaFold model)
Kinetochore protein SPC25	D	protein	115	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40014 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TCS_1 Kinetochore protein NDC80 (chains A)
SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLY
LRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNI
KLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSF
LKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDI
TSKFKINIQSSLENSENELGNVIEELRNLEFETEHNV

Sequence of entity 2 (B), FASTA

>5TCS_2 Kinetochore protein NUF2 (chains B)
SNASIFKDLEALSFQSNASRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVT
LYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGV
QDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFILQMESLLGQINKLNDEIKQ
LQKDFEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ

Sequence of entity 3 (C), FASTA

>5TCS_3 Kinetochore protein SPC24 (chains C)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARLKLYRSLGVILD
LENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Sequence of entity 4 (D), FASTA

>5TCS_4 Kinetochore protein SPC25 (chains D)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHVALYERLLQLRVLPGASDVHDVRFVFGDD
SRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Conserved Tetramer Junction in the Kinetochore Ndc80 Complex. Valverde, R., Ingram, J., Harrison, S.C. Cell Rep (2016) 17:1915-1922. DOI 10.1016/j.celrep.2016.10.065 · 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
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
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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