8Q85: Kinetochore protein NDC80
Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex. Determined by electron microscopy at 3.97 Å resolution. Released 6 Dec 2023.
- Method
- Electron microscopy
- Resolution
- 3.97 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 12
- Atoms
- 10,299
- Mol. weight
- 337.53 kDa
- Released
- 6 Dec 2023
Explore 8Q85 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8Q85 contains 60 α-helices and 9 β-strands across 12 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: 17 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-21 | 18 | |
| α-helix | 24-27 | 4 | |
| α-helix | 29-36 | 8 | |
| α-helix | 41-51 | 11 | |
| β-strand | 52-54 | 3 | 2 |
| α-helix | 55-56 | 2 | |
| α-helix | 57-63 | 7 | |
| β-strand | 64-67 | 4 | 3 |
| β-strand | 72-75 | 4 | 3 |
| α-helix | 82-98 | 17 | |
| α-helix | 101-104 | 4 | |
| α-helix | 112-124 | 13 | |
| α-helix | 159-167 | 9 | |
| α-helix | 172-182 | 11 | |
| β-strand | 185-189 | 5 | 4 |
| α-helix | 190 | 1 | |
| β-strand | 197-201 | 5 | 4 |
| α-helix | 202-204 | 3 | |
| α-helix | 207-220 | 14 | |
| α-helix | 224-236 | 13 | |
| α-helix | 237-241 | 5 | |
| α-helix | 242-264 | 23 | |
Chain b: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-34 | 31 | |
| α-helix | 35-39 | 5 | |
| α-helix | 40-56 | 17 | |
| α-helix | 58-68 | 11 | |
Chain c: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-35 | 33 | |
| α-helix | 36-46 | 11 | |
| α-helix | 47-62 | 16 | |
Chain d: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-39 | 38 | |
| β-strand | 44-45 | 2 | 1 |
| β-strand | 47-51 | 5 | 2 |
| α-helix | 52-64 | 13 | |
| α-helix | 66-107 | 42 | |
Chain F: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 435-477 | 43 | |
| α-helix | 485-488 | 4 | |
| α-helix | 507-510 | 4 | |
| α-helix | 517-521 | 5 | |
| α-helix | 522-662 | 141 | |
Chain G: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 271-302 | 32 | |
| α-helix | 303-309 | 7 | |
| α-helix | 310-335 | 26 | |
| α-helix | 336-341 | 6 | |
| α-helix | 342-382 | 41 | |
| α-helix | 383-387 | 5 | |
| α-helix | 388-396 | 9 | |
| α-helix | 397-407 | 11 | |
| α-helix | 408-445 | 38 | |
Chain U: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-109 | 52 | |
| β-strand | 112-113 | 2 | 1 |
| α-helix | 121-150 | 30 | |
Chain V: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-124 | 64 | |
| α-helix | 127-142 | 16 | |
| α-helix | 147-149 | 3 | |
| α-helix | 152-175 | 24 | |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Kinetochore protein NDC80 | F | protein | 691 | Saccharomyces cerevisiae | P40460 (AlphaFold model) |
| Kinetochore protein NUF2 | G | protein | 451 | Saccharomyces cerevisiae | P33895 (AlphaFold model) |
| DASH complex subunit DAM1 | U | protein | 343 | Saccharomyces cerevisiae | P53267 (AlphaFold model) |
| DASH complex subunit DUO1 | V | protein | 247 | Saccharomyces cerevisiae | P53168 (AlphaFold model) |
| DASH complex subunit DAD2 | W | protein | 133 | Saccharomyces cerevisiae | P36162 |
| DASH complex subunit DAD1 | X | protein | 94 | Saccharomyces cerevisiae | Q12248 |
| DASH complex subunit DAD4 | Y | protein | 72 | Saccharomyces cerevisiae | P69851 |
| DASH complex subunit DAD3 | Z | protein | 94 | Saccharomyces cerevisiae | P69850 |
| DASH complex subunit SPC34 | a | protein | 295 | Saccharomyces cerevisiae | P36131 |
| DASH complex subunit ASK1 | b | protein | 292 | Saccharomyces cerevisiae | P35734 |
| DASH complex subunit HSK3 | c | protein | 69 | Saccharomyces cerevisiae | P69852 |
| DASH complex subunit SPC19 | d | protein | 165 | Saccharomyces cerevisiae | Q03954 |
Sequence of entity 1 (F), FASTA
>8Q85_1 Kinetochore protein NDC80 (chains F)
MQSSTSTDQHVLHHMDPHRFTSQIPTATSSQLRRRNSTNQGLTDMINKSIARNTISGTGI
PTGGINKNKRTRSTVAGGTNGTALALNDKSNSRNSVSRLSINQLGSLQQHLSNRDPRPLR
DKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLYLRLDPGYGFT
KSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNIKLDMCLNKVD
RSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSFLKLEDNYEPS
MQELKLGFEKFVHIINTDIANLQTQNDNLYEKYQEVMKISQKIKTTREKWKALKSDSNKY
ENYVNAMKQKSQEWPGKLEKMKSECELKEEEIKALQSNISELHKILRKKGISTEQFELQN
QEREKLTRELDKINIQSDKLTSSIKSRKLEAEGIFKSLLDTLRQYDSSIQNLTRSRSQLG
HNVNDSSLKINISENLLDRDFHEGISYEQLFPKGSGINESIKKSILKLNDEIQERIKTIE
KDNITLEKDIKNLKHDINEKTQINEKLELELSEANSKFELSKQENERLLVAQRIEIEKME
KKINDSNLLMKTKISDAEELVTSTELKLEELKVDLNRKRYKLHQQVIHVIDITSKFKINI
QSSLENSENELGNVIEELRNLEFETEHNVTN
Sequence of entity 2 (G), FASTA
>8Q85_2 Kinetochore protein NUF2 (chains G)
MSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESL
LNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQ
RLLSAVVNYARFREERMFDCNSFILQMESLLGQLRSKFDDYNLIQQQLKQYEDVDGDNIP
DEQELQKLEEQNKELEIQLKKLTKIQETLSIDYNDYKISKQSIFKDLEALSFQIVELESN
RDKLIKISNTDMEELSEGIKELNDLLIQRKKTLDDLTAQQKNLQDTVTTFETIISELYDV
LRIISSEVQESNRTETELVGLKQNLINNKLKLMNVLETGIMYKLEILQEQLDLQLKNLEK
LSQDTKEESRLNDTKLMDLQIKYENEIKPKIDKTDIFIQEELISGKINKLNDEIKQLQKD
FEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ
Sequence of entity 3 (U), FASTA
>8Q85_3 DASH complex subunit DAM1 (chains U)
MSEDKAKLGTTRSATEYRLSIGSAPTSRRSSMGESSSLMKFADQEGLTSSVGEYNENTIQ
QLLLPKIRELSDSIITLDSNFTRLNFIHESLADLNESLGSLLYGIMSNSWCVEFSQAPHD
IQDDLIAIKQLKSLEDEKNNLVMELSNMERGIKRKKDEQGENDLAKASQNKQFNQPLFPS
SQVRKYRSYDNRDKRKPSKIGNNLQVENEEDYEDDTSSEASFVLNPTNIGMSKSSQGHVT
KTTRLNNNTNSKLRRKSILHTIRNSIASGADLPIENDNVVNLGDLHPNNRISLGSGAARV
VNGPVTKNRNSMFSGRAERKPTESRHSVAKKTEKKINTRPPFR
Sequence of entity 4 (V), FASTA
>8Q85_4 DASH complex subunit DUO1 (chains V)
MSEQSQLDDSTIDKLIPQIFNEMRSNLNNTTNKFPKSTGGGASDNISANSNSIRSFNSIT
TQSLLKESESLDKITAMIKNVTAALKNNLPVYVNQVHEVCKSTNSILDSWINIHSQAGYI
HKLMSDQTYLKLINDRLHNENVNTNDEDGSTLHNVIALKKKEILDLRQKLENRKGEKDAA
PAKPPNQGLNPRYGVQSGRRPVPSAGISNNGRVRKTHVPASKRPSGIPRVTNRWTKPTAS
SSRKMFR
Sequence of entity 5 (W), FASTA
>8Q85_5 DASH complex subunit DAD2 (chains W)
MDSIDEQIAIKRKELQSLQKITSLTDGLKIQLTELNEQIKEMGMNADSVAQLMNNWDSII
NNISQASLGLLQYAEGDYEIGPWKDSKKKESEQSNETGLEAQENDKNDEDNDEDEDLVPL
PETMVRIRVDGNE
Sequence of entity 6 (X), FASTA
>8Q85_6 DASH complex subunit DAD1 (chains X)
MMASTSNDEEKLISTTDKYFIEQRNIVLQEINETMNSILNGLNGLNISLESSIAVGREFQ
SVSDLWKTLYDGLESLSDEAPIDEQPTLSQSKTK
Sequence of entity 7 (Y), FASTA
>8Q85_7 DASH complex subunit DAD4 (chains Y)
MENPHEQVQANILSRIIGNVKRLNESVAILNQELVTINNRNKNLEIMGAICDNYHSSVQF
NLEATNNKKPPL
Sequence of entity 8 (Z), FASTA
>8Q85_8 DASH complex subunit DAD3 (chains Z)
MEHNLSPLQQEVLDKYKQLSLDLKALDETIKELNYSQHRQQHSQQETVSPDEILQEMRDI
EVKIGLVGTLLKGSVYSLILQRKQEQESLGSNSK
Sequence of entity 9 (a), FASTA
>8Q85_9 DASH complex subunit SPC34 (chains a)
MGESLDRCIDDINRAVDSMSTLYFKPPGIFHNAILQGASNKASIRKDITRLIKDCNHDEA
YLLFKVNPEKQSVSRRDGKEGVFDYVIKRDTDMKRNRRLGRPGEKPIIHVPKEVYLNKDR
LDLNNKRRRTATTSGGGLNGFIFDTDLIGSSVISNSSSGTFKALSAVFKDDPQIQRLLYA
LENGSVLMEEESNNQRRKTIFVEDFPTDLILKVMAEVTDLWPLTEFKQDYDQLYHNYEQL
SSKLRFIKKEVLLQDDRLKTMSQYHPSSSHDVAKIIRKEKDEIRRLEMEIANLQE
Sequence of entity 10 (b), FASTA
>8Q85_10 DASH complex subunit ASK1 (chains b)
MDSASKEETLEKLDQEITVNLQKIDSNLSFCFHKITQDIIPHVATYSEICERIMDSTEWL
GTMFQETGLVNLQANAAAPVGNAPVKSLVSNNVGIFPTSAEEASRQSQTDNGPNEADSAV
HVNRDVHSMFNNDSIDDFHTANITSTGQILKLPDSSDEDTGSEAVPSREQTDLTGEGHGG
ADDEQDESTIQRQSRKRKISLLLQQQYGSSSSMVPSPIVPNKMRKQLAHEEHINNDGDND
DENSNNIESSPLKQGHHHPKGQADDNNEGPDEEESTKEVPKPGTIIHFSTNR
Sequence of entity 11 (c), FASTA
>8Q85_11 DASH complex subunit HSK3 (chains c)
MNANKQRQYNQLAHELRELQTNLQETTKQLDIMSKQCNENLVGQLGKVHGSWLIGSYIYY
MEQMLGKTQ
Sequence of entity 12 (d), FASTA
>8Q85_12 DASH complex subunit SPC19 (chains d)
MTDALEQSVLALEGTVSVLKDSVESLKCANEPSTNLASTMLQTKRVFRLVPEYDVERSKL
DLIEEVEPLVRTLGDKLRKSMGRMQRELDTLQQTYELNDLRLKKNISMDDDDALNSPDMG
QEYEGRDADDVVMMASSTNEELEELKKLKEKKKQLENKLEILKQK
Primary citation
Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Muir, K.W., Batters, C., Dendooven, T. et al. Science (2023) 382:1184-1190. DOI 10.1126/science.adj8736 · 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
- 5TD8 7.53 Å, Crystal structure of an Extended Dwarf Ndc80 Complex
Browse structure collections
About this viewer
MolViewer shows 8Q85 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.