5TD8: Extended Dwarf Ndc80 Complex
Crystal structure of an Extended Dwarf Ndc80 Complex. Determined by X-ray diffraction at 7.53 Å resolution. Released 16 Nov 2016.
- Method
- X-ray diffraction
- Resolution
- 7.53 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos
- Chains
- 5
- Atoms
- 6,435
- Mol. weight
- 101.64 kDa
- Ligands
- HG
- Released
- 16 Nov 2016
Explore 5TD8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5TD8 contains 27 α-helices and 18 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: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 122-138 | 17 | |
| α-helix | 141-144 | 4 | |
| α-helix | 159-173 | 15 | |
| α-helix | 177-179 | 3 | |
| α-helix | 183-185 | 3 | |
| α-helix | 187-194 | 8 | |
| α-helix | 199-201 | 3 | |
| α-helix | 204-207 | 4 | |
| α-helix | 215-248 | 34 | |
| α-helix | 267-291 | 25 | |
| α-helix | 298-678 | 79 | |
Chain B: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-22 | 9 | |
| α-helix | 40-52 | 13 | |
| α-helix | 57-64 | 8 | |
| α-helix | 82-100 | 19 | |
| α-helix | 109-112 | 4 | |
| α-helix | 116-139 | 24 | |
| α-helix | 141-449 | 56 | |
Chain C: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| α-helix | 24-50 | 27 | |
| α-helix | 58-167 | 11 | |
| β-strand | 170-173 | 4 | 1 |
| β-strand | 178-181 | 4 | 1 |
| β-strand | 190-193 | 4 | 1 |
| α-helix | 200-211 | 12 | |
Chain D: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 7-145 | 47 | |
| β-strand | 147-151 | 5 | 2 |
| β-strand | 159-163 | 5 | 2 |
| β-strand | 169-173 | 5 | 2 |
| β-strand | 181 | 1 | 2 |
| α-helix | 190-201 | 12 | |
| α-helix | 206-220 | 15 | |
Chain E: 1 helix, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 3 |
| β-strand | 11-13 | 3 | 4 |
| β-strand | 19-26 | 8 | 3 |
| β-strand | 35-40 | 6 | 4 |
| β-strand | 47-52 | 6 | 4 |
| β-strand | 58-59 | 2 | 4 |
| β-strand | 69-74 | 6 | 3 |
| β-strand | 79-84 | 6 | 3 |
| α-helix | 89-91 | 3 | |
| β-strand | 93-99 | 7 | 4 |
| β-strand | 117-118 | 2 | 4 |
| β-strand | 122-126 | 5 | 4 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Kinetochore protein NDC80 | A | protein | 279 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40460 (AlphaFold model) |
| Kinetochore protein NUF2 | B | protein | 198 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33895 (AlphaFold model) |
| Kinetochore protein SPC24 | C | protein | 114 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q04477 (AlphaFold model) |
| Kinetochore protein SPC25 | D | protein | 129 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40014 (AlphaFold model) |
| nanobody | E | protein | 145 | Vicugna pacos | |
Sequence of entity 1 (A), FASTA
>5TD8_1 Kinetochore protein NDC80 (chains A)
SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLY
LRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNI
KLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSF
LKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDI
TSKFKINIQSSLENSENELGNVIEELRNLEFETEHNVTN
Sequence of entity 2 (B), FASTA
>5TD8_2 Kinetochore protein NUF2 (chains B)
MSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESL
LNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQ
RLLSAVVNYARFREERMFDCNSFILQMESLLGQINKLNDEIKQLQKDFEVEVKEIEIEYS
LLSGHINKYMNEMLEYMQ
Sequence of entity 3 (C), FASTA
>5TD8_3 Kinetochore protein SPC24 (chains C)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESN
KKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK
Sequence of entity 4 (D), FASTA
>5TD8_4 Kinetochore protein SPC25 (chains D)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQVALYERLLQLRVLPG
ASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVV
ARDMLLASL
Sequence of entity 5 (E), FASTA
>5TD8_5 nanobody (chains E)
MQVQLVESGGGLVHPGGSLRLSCAASGRTGSRHAVAWFRQAPGKERDFVASINAVGLVRN
YADSVLGRFSISRDFAKNEVYLQMNSLEPEDTAVYYCAARYYSGTYSSTYDRDDYDYWGQ
GTQVTVSSGGGLPETGGLEHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HG | Mercury (II) ion | Hg | 6 |
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
- 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
Browse structure collections
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