8V11: Saccharomyces cerevisiae Ipl1 peptide
Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex. Determined by X-ray diffraction at 3.95 Å resolution. Released 15 May 2024.
- Method
- X-ray diffraction
- Resolution
- 3.95 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 8
- Atoms
- 11,265
- Mol. weight
- 166.94 kDa
- Released
- 15 May 2024
Explore 8V11 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8V11 contains 60 α-helices and 13 β-strands across 8 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 | Sheet |
|---|
| 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 | 215-252 | 38 | |
| α-helix | 264-291 | 28 | |
| α-helix | 298-679 | 80 | |
Chain B: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 57-62 | 6 | |
| α-helix | 1009-1012 | 4 | |
| α-helix | 1013-1022 | 10 | |
| α-helix | 1030-1034 | 5 | |
| α-helix | 1041-1053 | 13 | |
| α-helix | 1057-1064 | 8 | |
| α-helix | 1084-1100 | 17 | |
| α-helix | 1108-1112 | 5 | |
| α-helix | 1116-1135 | 20 | |
| α-helix | 1136-1140 | 5 | |
| α-helix | 1141-1447 | 54 | |
Chain C: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| α-helix | 24-167 | 31 | |
| β-strand | 173 | 1 | 1 |
| β-strand | 178-179 | 2 | 1 |
| α-helix | 190-191 | 2 | |
| β-strand | 192-193 | 2 | 1 |
| α-helix | 203-209 | 7 | |
Chain D: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 |
| α-helix | 190-198 | 9 | |
| α-helix | 199-203 | 5 | |
| α-helix | 206-219 | 14 | |
Chain E: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 215-255 | 41 | |
| α-helix | 264-291 | 28 | |
| α-helix | 298-679 | 80 | |
Chain F: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 57-64 | 8 | |
| α-helix | 1013-1020 | 8 | |
| α-helix | 1021-1025 | 5 | |
| α-helix | 1041-1053 | 13 | |
| α-helix | 1057-1066 | 10 | |
| α-helix | 1079-1099 | 21 | |
| α-helix | 1108-1112 | 5 | |
| α-helix | 1116-1136 | 21 | |
| α-helix | 1137-1140 | 4 | |
| α-helix | 1141-1448 | 55 | |
Chain G: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-21 | 11 | |
| α-helix | 24-167 | 31 | |
| β-strand | 171-173 | 3 | 3 |
| β-strand | 178-180 | 3 | 3 |
| α-helix | 190-191 | 2 | |
| β-strand | 192-193 | 2 | 3 |
| α-helix | 203-209 | 7 | |
Chain H: 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 | 4 |
| β-strand | 159-163 | 5 | 4 |
| β-strand | 169-173 | 5 | 4 |
| β-strand | 184 | 1 | 4 |
| 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, E | protein | 272 | Saccharomyces cerevisiae | P40460 (AlphaFold model) |
| Ipl1/Nuf2 chimera protein | B, F | protein | 227 | Saccharomyces cerevisiae | P33895 (AlphaFold model), P38991 (AlphaFold model) |
| Kinetochore protein SPC24 | C, G | protein | 99 | Saccharomyces cerevisiae | Q04477 (AlphaFold model) |
| Kinetochore protein SPC25 | D, H | protein | 114 | Saccharomyces cerevisiae | P40014 |
Sequence of entity 1 (A, E), FASTA
>8V11_1 Kinetochore protein NDC80 (chains A, E)
SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLY
LRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNI
KLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSF
LKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDI
TSKFKINIQSSLENSENELGNVIEELRNLEFE
Sequence of entity 2 (B, F), FASTA
>8V11_2 Ipl1/Nuf2 chimera protein (chains B, F)
MTSRINKPWRISHSPNSKIPSPVREKLNRLSRNQDVFPILDLQELVICLQSCDFALATQE
NISRPTSDYMVTLYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTLNVLVLN
KICFKFFENIGVQDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFILQMESLL
GQINKLNDEIKQLQKDFEVEVKEIEAAYSLLSGHINKYMNEMLEYMQ
Sequence of entity 3 (C, G), FASTA
>8V11_3 Kinetochore protein SPC24 (chains C, G)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARLKLYRSLGVILD
LENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLG
Sequence of entity 4 (D, H), FASTA
>8V11_4 Kinetochore protein SPC25 (chains D, H)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHVALYERLLQLRVLPGASDVHDVRFVFGDD
SRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLAS
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
- 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
- 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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