8QAU: Tubulin alpha-1A chain
Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex. Determined by electron microscopy at 3.54 Å resolution. Released 3 Apr 2024.
- Method
- Electron microscopy
- Resolution
- 3.54 Å
- Organisms
- Sus scrofa, Saccharomyces cerevisiae
- Chains
- 5
- Atoms
- 10,137
- Mol. weight
- 273.99 kDa
- Ligands
- TA1, GDP, MG, GTP
- Released
- 3 Apr 2024
Explore 8QAU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QAU contains 71 α-helices and 37 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: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 123-138 | 16 | |
| α-helix | 141-144 | 4 | |
| α-helix | 151-155 | 5 | |
| α-helix | 159-171 | 13 | |
| α-helix | 183-193 | 11 | |
| α-helix | 199-201 | 3 | |
| α-helix | 204-208 | 5 | |
| α-helix | 215-254 | 40 | |
| α-helix | 261-291 | 31 | |
| α-helix | 298-364 | 67 | |
Chain B: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 13-23 | 11 | |
| α-helix | 30-34 | 5 | |
| α-helix | 38-52 | 15 | |
| α-helix | 57-69 | 13 | |
| α-helix | 78-100 | 23 | |
| α-helix | 108-112 | 5 | |
| α-helix | 116-139 | 24 | |
| α-helix | 141-168 | 28 | |
| α-helix | 182-206 | 25 | |
Chain C: 26 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-8 | 7 | 1 |
| α-helix | 10-27 | 18 | |
| β-strand | 35 | 1 | 2 |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 3 |
| β-strand | 60 | 1 | 2 |
| β-strand | 61-63 | 3 | 3 |
| β-strand | 65-68 | 4 | 1 |
| α-helix | 73-80 | 8 | |
| β-strand | 92-93 | 2 | 1 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 111-113 | 3 | |
| α-helix | 115-128 | 14 | |
| β-strand | 131-138 | 8 | 1 |
| α-helix | 145-149 | 5 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-169 | 5 | 1 |
| β-strand | 172 | 1 | 4 |
| α-helix | 173-174 | 2 | |
| α-helix | 183-189 | 7 | |
| α-helix | 191-195 | 5 | |
| β-strand | 202 | 1 | 1 |
| β-strand | 203 | 1 | 5 |
| β-strand | 205 | 1 | 4 |
| α-helix | 206-215 | 10 | |
| α-helix | 224-239 | 16 | |
| α-helix | 240-242 | 3 | |
| β-strand | 248 | 1 | 5 |
| α-helix | 252-259 | 8 | |
| β-strand | 269-273 | 5 | 5 |
| α-helix | 278-283 | 6 | |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 5 |
| α-helix | 325-337 | 13 | |
| β-strand | 343 | 1 | 5 |
| β-strand | 351-356 | 6 | 5 |
| α-helix | 359-361 | 3 | |
| α-helix | 369-370 | 2 | |
| β-strand | 373-381 | 9 | 5 |
| α-helix | 385-399 | 15 | |
| α-helix | 406-409 | 4 | |
| α-helix | 416-431 | 16 | |
Chain D: 24 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 6 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 7 |
| β-strand | 35 | 1 | 8 |
| β-strand | 36 | 1 | 7 |
| α-helix | 47-49 | 3 | |
| β-strand | 51-54 | 4 | 8 |
| β-strand | 58-61 | 4 | 8 |
| β-strand | 63-67 | 5 | 6 |
| α-helix | 70-77 | 8 | |
| α-helix | 82-84 | 3 | |
| α-helix | 87-89 | 3 | |
| β-strand | 91-92 | 2 | 6 |
| α-helix | 101-102 | 2 | |
| α-helix | 103-107 | 5 | |
| α-helix | 110-125 | 16 | |
| β-strand | 130-138 | 9 | 6 |
| α-helix | 143-158 | 16 | |
| β-strand | 163-170 | 8 | 6 |
| α-helix | 181-194 | 14 | |
| β-strand | 198-203 | 6 | 6 |
| α-helix | 204-209 | 6 | |
| α-helix | 210-214 | 5 | |
| α-helix | 222-236 | 15 | |
| α-helix | 238-241 | 4 | |
| β-strand | 246 | 1 | 9 |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 6 |
| β-strand | 267-271 | 5 | 9 |
| α-helix | 283-284 | 2 | |
| α-helix | 286-293 | 8 | |
| α-helix | 305-307 | 3 | |
| β-strand | 310-318 | 9 | 9 |
| α-helix | 323-336 | 14 | |
| β-strand | 341 | 1 | 9 |
| β-strand | 349-354 | 6 | 9 |
| α-helix | 357-358 | 2 | |
| β-strand | 364-371 | 8 | 9 |
| α-helix | 372-374 | 3 | |
| α-helix | 375-389 | 15 | |
| α-helix | 395-401 | 7 | |
| α-helix | 405-426 | 22 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 258-266 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Tubulin alpha-1A chain | C | protein | 451 | Sus scrofa | P02550 (AlphaFold model) |
| Tubulin beta chain | D | protein | 445 | Sus scrofa | P02554 (AlphaFold model) |
| Kinetochore protein NDC80 | A | protein | 691 | Saccharomyces cerevisiae | P40460 (AlphaFold model) |
| Kinetochore protein NUF2 | B | protein | 451 | Saccharomyces cerevisiae | P33895 (AlphaFold model) |
| DASH complex subunit DAM1 | E | protein | 343 | Saccharomyces cerevisiae | P53267 |
Sequence of entity 1 (C), FASTA
>8QAU_1 Tubulin alpha-1A chain (chains C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Sequence of entity 2 (D), FASTA
>8QAU_2 Tubulin beta chain (chains D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA
Sequence of entity 3 (A), FASTA
>8QAU_3 Kinetochore protein NDC80 (chains A)
MQSSTSTDQHVLHHMDPHRFTSQIPTATSSQLRRRNSTNQGLTDMINKSIARNTISGTGI
PTGGINKNKRTRSTVAGGTNGTALALNDKSNSRNSVSRLSINQLGSLQQHLSNRDPRPLR
DKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLYLRLDPGYGFT
KSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNIKLDMCLNKVD
RSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSFLKLEDNYEPS
MQELKLGFEKFVHIINTDIANLQTQNDNLYEKYQEVMKISQKIKTTREKWKALKSDSNKY
ENYVNAMKQKSQEWPGKLEKMKSECELKEEEIKALQSNISELHKILRKKGISTEQFELQN
QEREKLTRELDKINIQSDKLTSSIKSRKLEAEGIFKSLLDTLRQYDSSIQNLTRSRSQLG
HNVNDSSLKINISENLLDRDFHEGISYEQLFPKGSGINESIKKSILKLNDEIQERIKTIE
KDNITLEKDIKNLKHDINEKTQINEKLELELSEANSKFELSKQENERLLVAQRIEIEKME
KKINDSNLLMKTKISDAEELVTSTELKLEELKVDLNRKRYKLHQQVIHVIDITSKFKINI
QSSLENSENELGNVIEELRNLEFETEHNVTN
Sequence of entity 4 (B), FASTA
>8QAU_4 Kinetochore protein NUF2 (chains B)
MSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESL
LNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQ
RLLSAVVNYARFREERMFDCNSFILQMESLLGQLRSKFDDYNLIQQQLKQYEDVDGDNIP
DEQELQKLEEQNKELEIQLKKLTKIQETLSIDYNDYKISKQSIFKDLEALSFQIVELESN
RDKLIKISNTDMEELSEGIKELNDLLIQRKKTLDDLTAQQKNLQDTVTTFETIISELYDV
LRIISSEVQESNRTETELVGLKQNLINNKLKLMNVLETGIMYKLEILQEQLDLQLKNLEK
LSQDTKEESRLNDTKLMDLQIKYENEIKPKIDKTDIFIQEELISGKINKLNDEIKQLQKD
FEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ
Sequence of entity 5 (E), FASTA
>8QAU_5 DASH complex subunit DAM1 (chains E)
MSEDKAKLGTTRSATEYRLSIGSAPTSRRSSMGESSSLMKFADQEGLTSSVGEYNENTIQ
QLLLPKIRELSDSIITLDSNFTRLNFIHESLADLNESLGSLLYGIMSNSWCVEFSQAPHD
IQDDLIAIKQLKSLEDEKNNLVMELSNMERGIKRKKDEQGENDLAKASQNKQFNQPLFPS
SQVRKYRSYDNRDKRKPSKIGNNLQVENEEDYEDDTSSEASFVLNPTNIGMSKSSQGHVT
KTTRLNNNTNSKLRRKSILHTIRNSIASGADLPIENDNVVNLGDLHPNNRISLGSGAARV
VNGPVTKNRNSMFSGRAERKPTESRHSVAKKTEKKINTRPPFR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| TA1 | Taxol | C47 H51 N O14 | 1 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
| MG | Magnesium ion | Mg | 1 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
Primary citation
Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction. Muir, K.W., Batters, C., Dendooven, T. et al. bioRxiv (2023). DOI 10.1101/2023.07.20.549907
Other PDB entries of the same protein (UniProt P02550 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7X4N 2.88 Å, Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with tubulin and DARPin
- 9T1D 2.9 Å, Cryo-EM reconstruction of undecorated GDP microtubule
- 6MZG 3.21 Å, Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with…
- 7U0F 3.53 Å, HIV-1 Rev in complex with tubulin
- 8X9P 3.54 Å, HURP (428-534)-alpha-tubulin-beta-tubulin complex
- 6MZE 3.6 Å, Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with…
- 6KIQ 3.62 Å, Complex of yeast cytoplasmic dynein MTBD-High and MT with DTT
- 1TUB 3.7 Å, Tubulin alpha-beta dimer, electron diffraction
- 9EDT 3.7 Å, Tubulin cofactors D,E,G bound to tubulin dimer
- 9EEB 3.7 Å, Tubulin cofactors D,E,G bound to tubulin dimer
- 9EDR 3.8 Å, Tubulin Cofactors D,E,G,C and Tubulin complex -- TBCC N Terminus Bound to Tubulin
- 9EDS 3.8 Å, Tubulin cofactors D,E,G,C bound to tubulin dimer -- TBCC N terminus unbound
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