8Q84: Kinetochore protein NDC80
Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex. Determined by electron microscopy at 3.15 Å resolution. Released 6 Dec 2023.
- Method
- Electron microscopy
- Resolution
- 3.15 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 25
- Atoms
- 21,802
- Mol. weight
- 713.54 kDa
- Released
- 6 Dec 2023
Explore 8Q84 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8Q84 contains 126 α-helices and 18 β-strands across 24 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: 16 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-21 | 18 | |
| α-helix | 24-27 | 4 | |
| α-helix | 30-36 | 7 | |
| α-helix | 41-51 | 11 | |
| β-strand | 52-54 | 3 | 6 |
| α-helix | 55-56 | 2 | |
| α-helix | 57-63 | 7 | |
| β-strand | 64-67 | 4 | 7 |
| β-strand | 72-75 | 4 | 7 |
| 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 | 8 |
| α-helix | 190 | 1 | |
| β-strand | 197-201 | 5 | 8 |
| α-helix | 207-220 | 14 | |
| α-helix | 224-236 | 13 | |
| α-helix | 237-241 | 5 | |
| α-helix | 242-264 | 23 | |
Chains A and F: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 373-392 | 20 | |
| α-helix | 395-408 | 14 | |
| α-helix | 416-478 | 63 | |
| α-helix | 485-488 | 4 | |
| α-helix | 496-498 | 3 | |
| α-helix | 507-510 | 4 | |
| α-helix | 517-521 | 5 | |
| α-helix | 522-662 | 141 | |
Chain b: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-34 | 32 | |
| α-helix | 35-39 | 5 | |
| α-helix | 40-56 | 17 | |
| α-helix | 58-68 | 11 | |
Chain B: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 212-243 | 32 | |
| α-helix | 245-247 | 3 | |
| α-helix | 253-303 | 51 | |
| α-helix | 304-308 | 5 | |
| α-helix | 309-335 | 27 | |
| α-helix | 336-340 | 5 | |
| α-helix | 341-382 | 42 | |
| α-helix | 383-387 | 5 | |
| α-helix | 388-396 | 9 | |
| α-helix | 397-407 | 11 | |
| α-helix | 408-445 | 38 | |
Chain c: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-34 | 32 | |
| α-helix | 35-46 | 12 | |
| α-helix | 47-62 | 16 | |
Chain d: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-39 | 38 | |
| β-strand | 44-45 | 2 | 5 |
| β-strand | 47-51 | 5 | 6 |
| α-helix | 52-61 | 10 | |
| α-helix | 62-66 | 5 | |
| α-helix | 67-107 | 41 | |
Chain G: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 213-243 | 31 | |
| α-helix | 244-247 | 4 | |
| α-helix | 253-302 | 50 | |
| α-helix | 303-309 | 7 | |
| α-helix | 310-335 | 26 | |
| α-helix | 336-340 | 5 | |
| α-helix | 341-382 | 42 | |
| α-helix | 383-387 | 5 | |
| α-helix | 388-396 | 9 | |
| α-helix | 397-407 | 11 | |
| α-helix | 408-445 | 38 | |
Chain I: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-109 | 52 | |
| β-strand | 112-114 | 3 | 1 |
| α-helix | 121-150 | 30 | |
14 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 | A, F | protein | 691 | Saccharomyces cerevisiae | P40460 (AlphaFold model) |
| Kinetochore protein NUF2 | B, G | protein | 451 | Saccharomyces cerevisiae | P33895 (AlphaFold model) |
| DASH complex subunit DAM1 | I, U, e | protein | 343 | Saccharomyces cerevisiae | P53267 (AlphaFold model) |
| DASH complex subunit DUO1 | J, V | protein | 247 | Saccharomyces cerevisiae | P53168 (AlphaFold model) |
| DASH complex subunit DAD2 | K, W | protein | 133 | Saccharomyces cerevisiae | P36162 |
| DASH complex subunit DAD1 | L, X | protein | 94 | Saccharomyces cerevisiae | Q12248 |
| DASH complex subunit DAD4 | M, Y | protein | 72 | Saccharomyces cerevisiae | P69851 |
| DASH complex subunit DAD3 | N, Z | protein | 94 | Saccharomyces cerevisiae | P69850 |
| DASH complex subunit SPC34 | O, a | protein | 295 | Saccharomyces cerevisiae | P36131 |
| DASH complex subunit ASK1 | P, b | protein | 292 | Saccharomyces cerevisiae | P35734 |
| DASH complex subunit HSK3 | Q, c | protein | 69 | Saccharomyces cerevisiae | P69852 |
| DASH complex subunit SPC19 | R, d | protein | 165 | Saccharomyces cerevisiae | Q03954 |
Sequence of entity 1 (A, F), FASTA
>8Q84_1 Kinetochore protein NDC80 (chains A, F)
MQSSTSTDQHVLHHMDPHRFTSQIPTATSSQLRRRNSTNQGLTDMINKSIARNTISGTGI
PTGGINKNKRTRSTVAGGTNGTALALNDKSNSRNSVSRLSINQLGSLQQHLSNRDPRPLR
DKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLYLRLDPGYGFT
KSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNIKLDMCLNKVD
RSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSFLKLEDNYEPS
MQELKLGFEKFVHIINTDIANLQTQNDNLYEKYQEVMKISQKIKTTREKWKALKSDSNKY
ENYVNAMKQKSQEWPGKLEKMKSECELKEEEIKALQSNISELHKILRKKGISTEQFELQN
QEREKLTRELDKINIQSDKLTSSIKSRKLEAEGIFKSLLDTLRQYDSSIQNLTRSRSQLG
HNVNDSSLKINISENLLDRDFHEGISYEQLFPKGSGINESIKKSILKLNDEIQERIKTIE
KDNITLEKDIKNLKHDINEKTQINEKLELELSEANSKFELSKQENERLLVAQRIEIEKME
KKINDSNLLMKTKISDAEELVTSTELKLEELKVDLNRKRYKLHQQVIHVIDITSKFKINI
QSSLENSENELGNVIEELRNLEFETEHNVTN
Sequence of entity 2 (B, G), FASTA
>8Q84_2 Kinetochore protein NUF2 (chains B, G)
MSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESL
LNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQ
RLLSAVVNYARFREERMFDCNSFILQMESLLGQLRSKFDDYNLIQQQLKQYEDVDGDNIP
DEQELQKLEEQNKELEIQLKKLTKIQETLSIDYNDYKISKQSIFKDLEALSFQIVELESN
RDKLIKISNTDMEELSEGIKELNDLLIQRKKTLDDLTAQQKNLQDTVTTFETIISELYDV
LRIISSEVQESNRTETELVGLKQNLINNKLKLMNVLETGIMYKLEILQEQLDLQLKNLEK
LSQDTKEESRLNDTKLMDLQIKYENEIKPKIDKTDIFIQEELISGKINKLNDEIKQLQKD
FEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ
Sequence of entity 3 (I, U, e), FASTA
>8Q84_3 DASH complex subunit DAM1 (chains I, U, e)
MSEDKAKLGTTRSATEYRLSIGSAPTSRRSSMGESSSLMKFADQEGLTSSVGEYNENTIQ
QLLLPKIRELSDSIITLDSNFTRLNFIHESLADLNESLGSLLYGIMSNSWCVEFSQAPHD
IQDDLIAIKQLKSLEDEKNNLVMELSNMERGIKRKKDEQGENDLAKASQNKQFNQPLFPS
SQVRKYRSYDNRDKRKPSKIGNNLQVENEEDYEDDTSSEASFVLNPTNIGMSKSSQGHVT
KTTRLNNNTNSKLRRKSILHTIRNSIASGADLPIENDNVVNLGDLHPNNRISLGSGAARV
VNGPVTKNRNSMFSGRAERKPTESRHSVAKKTEKKINTRPPFR
Sequence of entity 4 (J, V), FASTA
>8Q84_4 DASH complex subunit DUO1 (chains J, V)
MSEQSQLDDSTIDKLIPQIFNEMRSNLNNTTNKFPKSTGGGASDNISANSNSIRSFNSIT
TQSLLKESESLDKITAMIKNVTAALKNNLPVYVNQVHEVCKSTNSILDSWINIHSQAGYI
HKLMSDQTYLKLINDRLHNENVNTNDEDGSTLHNVIALKKKEILDLRQKLENRKGEKDAA
PAKPPNQGLNPRYGVQSGRRPVPSAGISNNGRVRKTHVPASKRPSGIPRVTNRWTKPTAS
SSRKMFR
Sequence of entity 5 (K, W), FASTA
>8Q84_5 DASH complex subunit DAD2 (chains K, W)
MDSIDEQIAIKRKELQSLQKITSLTDGLKIQLTELNEQIKEMGMNADSVAQLMNNWDSII
NNISQASLGLLQYAEGDYEIGPWKDSKKKESEQSNETGLEAQENDKNDEDNDEDEDLVPL
PETMVRIRVDGNE
Sequence of entity 6 (L, X), FASTA
>8Q84_6 DASH complex subunit DAD1 (chains L, X)
MMASTSNDEEKLISTTDKYFIEQRNIVLQEINETMNSILNGLNGLNISLESSIAVGREFQ
SVSDLWKTLYDGLESLSDEAPIDEQPTLSQSKTK
Sequence of entity 7 (M, Y), FASTA
>8Q84_7 DASH complex subunit DAD4 (chains M, Y)
MENPHEQVQANILSRIIGNVKRLNESVAILNQELVTINNRNKNLEIMGAICDNYHSSVQF
NLEATNNKKPPL
Sequence of entity 8 (N, Z), FASTA
>8Q84_8 DASH complex subunit DAD3 (chains N, Z)
MEHNLSPLQQEVLDKYKQLSLDLKALDETIKELNYSQHRQQHSQQETVSPDEILQEMRDI
EVKIGLVGTLLKGSVYSLILQRKQEQESLGSNSK
Sequence of entity 9 (O, a), FASTA
>8Q84_9 DASH complex subunit SPC34 (chains O, a)
MGESLDRCIDDINRAVDSMSTLYFKPPGIFHNAILQGASNKASIRKDITRLIKDCNHDEA
YLLFKVNPEKQSVSRRDGKEGVFDYVIKRDTDMKRNRRLGRPGEKPIIHVPKEVYLNKDR
LDLNNKRRRTATTSGGGLNGFIFDTDLIGSSVISNSSSGTFKALSAVFKDDPQIQRLLYA
LENGSVLMEEESNNQRRKTIFVEDFPTDLILKVMAEVTDLWPLTEFKQDYDQLYHNYEQL
SSKLRFIKKEVLLQDDRLKTMSQYHPSSSHDVAKIIRKEKDEIRRLEMEIANLQE
Sequence of entity 10 (P, b), FASTA
>8Q84_10 DASH complex subunit ASK1 (chains P, b)
MDSASKEETLEKLDQEITVNLQKIDSNLSFCFHKITQDIIPHVATYSEICERIMDSTEWL
GTMFQETGLVNLQANAAAPVGNAPVKSLVSNNVGIFPTSAEEASRQSQTDNGPNEADSAV
HVNRDVHSMFNNDSIDDFHTANITSTGQILKLPDSSDEDTGSEAVPSREQTDLTGEGHGG
ADDEQDESTIQRQSRKRKISLLLQQQYGSSSSMVPSPIVPNKMRKQLAHEEHINNDGDND
DENSNNIESSPLKQGHHHPKGQADDNNEGPDEEESTKEVPKPGTIIHFSTNR
Sequence of entity 11 (Q, c), FASTA
>8Q84_11 DASH complex subunit HSK3 (chains Q, c)
MNANKQRQYNQLAHELRELQTNLQETTKQLDIMSKQCNENLVGQLGKVHGSWLIGSYIYY
MEQMLGKTQ
Sequence of entity 12 (R, d), FASTA
>8Q84_12 DASH complex subunit SPC19 (chains R, 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
- 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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