7KDF: Stu2

Structure of Stu2 Bound to dwarf Ndc80c. Determined by X-ray diffraction at 2.72 Å resolution. Released 11 Nov 2020.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 5,994
Mol. weight: 87.17 kDa
Released: 11 Nov 2020

Explore 7KDF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KDF contains 33 α-helices and 7 β-strands across 5 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: 12 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	183-185	3
α-helix	187-194	8
α-helix	204-207	4
α-helix	215-246	32
α-helix	249-254	6
α-helix	257-258	2
α-helix	267-291	25
α-helix	298-679	80

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	8-11	4
α-helix	12-21	10
α-helix	29-33	5
α-helix	39-52	14
α-helix	56-64	9
α-helix	78-98	21
α-helix	107-111	5
α-helix	115-135	21
α-helix	136-139	4
α-helix	140-447	55

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	24-167	31
β-strand	171-173	3	1
β-strand	178-180	3	1
α-helix	189-191	3
β-strand	192-193	2	1
α-helix	203-209	7

Chain D: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-24	18
α-helix	139-145	7
β-strand	147-151	5	2
β-strand	159-163	5	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

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	865-881	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NDC80 isoform 1,NDC80 isoform 1	A	protein	277	Saccharomyces cerevisiae	P40460 (AlphaFold model)
NUF2 isoform 1,NUF2 isoform 1	B	protein	215	Saccharomyces cerevisiae	P33895 (AlphaFold model)
Spc24	C	protein	100	Saccharomyces cerevisiae	Q04477 (AlphaFold model)
SPC25 isoform 1,SPC25 isoform 1	D	protein	115	Saccharomyces cerevisiae	P40014 (AlphaFold model)
STU2	E	protein	33	Saccharomyces cerevisiae	P46675

Sequence of entity 1 (A), FASTA

>7KDF_1 NDC80 isoform 1,NDC80 isoform 1 (chains A)
SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLY
LRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNI
KLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSF
LKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDI
TSKFKINIQSSLENSENELGNVIEELRNLEFETEHNV

Sequence of entity 2 (B), FASTA

>7KDF_2 NUF2 isoform 1,NUF2 isoform 1 (chains B)
SNASIFKDLEALSFQSNASRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVT
LYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGV
QDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFILQMESLLGQINKLNDEIKQ
LQKDFEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ

Sequence of entity 3 (C), FASTA

>7KDF_3 Spc24 (chains C)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARLKLYRSLGVILD
LENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Sequence of entity 4 (D), FASTA

>7KDF_4 SPC25 isoform 1,SPC25 isoform 1 (chains D)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHVALYERLLQLRVLPGASDVHDVRFVFGDD
SRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Sequence of entity 5 (E), FASTA

>7KDF_5 STU2 (chains E)
EESYKRAAAVTSTLKARIEKMKAKSRREGTTRT

Primary citation

Structural basis of Stu2 recruitment to yeast kinetochores. Zahm, J.A., Stewart, M.G., Carrier, J.S. et al. Elife (2021) 10. DOI 10.7554/eLife.65389 · PubMed

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

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
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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