6KIQ: Alpha tubulin

Complex of yeast cytoplasmic dynein MTBD-High and MT with DTT. Determined by electron microscopy at 3.62 Å resolution. Released 4 Mar 2020.

Method: Electron microscopy
Resolution: 3.62 Å
Organisms: Sus scrofa, Saccharomyces cerevisiae S288c
Chains: 3
Atoms: 7,649
Mol. weight: 109.03 kDa
Released: 4 Mar 2020

Explore 6KIQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KIQ contains 54 α-helices and 37 β-strands across 3 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: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	1006-1009	4	1
α-helix	1011-1028	18
β-strand	1040-1043	4	1
α-helix	1047-1054	8
α-helix	1063-1065	3
β-strand	1066-1068	3	1
α-helix	1077-1081	5
α-helix	1083-1100	18
β-strand	1108-1111	4	1
β-strand	1114	1	1
α-helix	1122-1134	13
β-strand	1139-1145	7	1
α-helix	1157-1169	13
β-strand	1174-1178	5	1
α-helix	1180-1189	10
α-helix	1198-1216	19
β-strand	1222	1	2
α-helix	1226-1232	7
β-strand	1242-1243	2	3
α-helix	1262-1270	9
α-helix	1281-1283	3
α-helix	1284	1
β-strand	1285	1	4
β-strand	1286-1289	4	3
β-strand	1292-1295	4	2
α-helix	1299-1310	12
β-strand	1316	1	4
β-strand	1328-1330	3	2
β-strand	1347-1350	4	2
β-strand	1353-1355	3	3
α-helix	1356-1358	3
α-helix	1359-1375	17
α-helix	1380-1383	4
α-helix	1389-1403	15
α-helix	1405-1408	4

Chain b: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	8-9	2	6
α-helix	11-26	16
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-44	4
α-helix	49-51	3
β-strand	55-56	2	8
β-strand	60-61	2	8
β-strand	67-69	3	6
α-helix	75-78	4
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	104-106	3
α-helix	111-114	4
α-helix	116-126	11
β-strand	132-139	8	5
α-helix	144	1
α-helix	145-150	6
α-helix	151-160	10
β-strand	165-170	6	5
α-helix	183-194	12
β-strand	200-202	3	5
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-237	14
α-helix	240-243	4
α-helix	252-257	6
β-strand	267-268	2	5
β-strand	269-271	3	9
α-helix	278-280	3
α-helix	289-295	7
α-helix	307-309	3
β-strand	312	1	10
β-strand	315	1	11
β-strand	318-319	2	12
α-helix	325-338	14
α-helix	340-342	3
β-strand	351	1	11
β-strand	354-355	2	12
β-strand	375-376	2	12
β-strand	377-379	3	9
β-strand	381	1	10
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	416-434	19

Chain M: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	3104-3113	10
α-helix	3117-3125	9
α-helix	3131-3144	14
α-helix	3151-3158	8
α-helix	3162-3169	8
α-helix	3180-3184	5
α-helix	3185-3189	5
α-helix	3196-3202	7
α-helix	3206-3218	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha tubulin	a	protein	412	Sus scrofa	P02550 (AlphaFold model)
Tubulin beta chain	b	protein	426	Sus scrofa	P02554 (AlphaFold model)
Dynein heavy chain, cytoplasmic	M	protein	130	Saccharomyces cerevisiae S288c	P36022

Sequence of entity 1 (a), FASTA

>6KIQ_1 Alpha tubulin (chains a)
RECISIHVGQAGVQIGNACWELYCLEHGIQPDGHVPRAVFVDLEPTVIDEVRTGTYRQLF
HPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGS
GFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
AIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHF
PLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKD
VNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEA
WARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS

Sequence of entity 2 (b), FASTA

>6KIQ_2 Tubulin beta chain (chains b)
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVP
RAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVR
KESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVE
PYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLR
FPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMA
ACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGL
KMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSE
YQQYQD

Sequence of entity 3 (M), FASTA

>6KIQ_3 Dynein heavy chain, cytoplasmic (chains M)
MKSIQDCEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDI
QQFIRKDDFIHNIVHYDTTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVN
AQINFSKCLE

Primary citation

Structural basis for two-way communication between dynein and microtubules. Nishida, N., Komori, Y., Takarada, O. et al. Nat Commun (2020) 11:1038-1038. DOI 10.1038/s41467-020-14842-8 · PubMed

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
8QAU 3.54 Å, Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
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…
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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