6KIO: Tubulin beta chain

Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT. Determined by electron microscopy at 3.94 Å resolution. Released 4 Mar 2020.

Method: Electron microscopy
Resolution: 3.94 Å
Organisms: Sus scrofa, Saccharomyces cerevisiae S288c
Chains: 3
Atoms: 7,649
Mol. weight: 109.03 kDa
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6KIO contains 54 α-helices and 35 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1006-1009	4	7
α-helix	1011-1028	18
β-strand	1039-1043	5	7
α-helix	1047-1054	8
α-helix	1063-1065	3
β-strand	1066-1068	3	7
α-helix	1077-1081	5
α-helix	1083-1102	20
β-strand	1108-1114	7	7
α-helix	1118-1134	17
β-strand	1139-1145	7	7
α-helix	1157-1169	13
β-strand	1174-1178	5	7
α-helix	1180-1189	10
α-helix	1198-1216	19
β-strand	1222	1	8
α-helix	1226-1233	8
β-strand	1243-1246	4	8
β-strand	1251	1	9
α-helix	1262-1267	6
α-helix	1272-1274	3
α-helix	1281-1283	3
β-strand	1286-1295	10	8
α-helix	1299-1310	12
β-strand	1317	1	8
β-strand	1325-1330	6	8
β-strand	1342	1	9
β-strand	1347-1355	9	8
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	4-9	6	1
α-helix	11-26	16
β-strand	30	1	2
β-strand	36	1	2
α-helix	41-47	5
α-helix	49-52	4
β-strand	55	1	3
β-strand	61	1	3
β-strand	65-66	2	1
β-strand	67-69	3	4
α-helix	75-78	4
α-helix	89-91	3
β-strand	92-94	3	4
α-helix	103-107	5
α-helix	111-114	4
α-helix	116-126	11
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-150	6
α-helix	151-160	10
β-strand	165-171	7	1
α-helix	183-194	12
β-strand	200-203	4	1
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	5
α-helix	252-257	6
β-strand	267-268	2	1
β-strand	269-271	3	6
α-helix	279-281	3
α-helix	289-295	7
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-315	4	6
β-strand	318-320	3	5
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	6
β-strand	351	1	6
β-strand	354-356	3	5
β-strand	374-376	3	5
β-strand	377-381	5	6
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-434	20

Chain M: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	3102-3112	11
α-helix	3117-3125	9
α-helix	3131-3144	14
α-helix	3151-3159	9
α-helix	3163-3169	7
α-helix	3180-3184	5
α-helix	3185-3189	5
α-helix	3196-3202	7
α-helix	3207-3218	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta chain	b	protein	426	Sus scrofa	P02554 (AlphaFold model)
Dynein heavy chain, cytoplasmic	M	protein	130	Saccharomyces cerevisiae S288c	P36022
Tubulin alpha-1A chain	a	protein	412	Sus scrofa	P02550 (AlphaFold model)

Sequence of entity 1 (b), FASTA

>6KIO_1 Tubulin beta chain (chains b)
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVP
RAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVR
KESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVE
PYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLR
FPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMA
ACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGL
KMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSE
YQQYQD

Sequence of entity 2 (M), FASTA

>6KIO_2 Dynein heavy chain, cytoplasmic (chains M)
MKSIQDCEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDI
QQFIRKDDFIHNIVHYDTTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVN
AQINFSKCLE

Sequence of entity 3 (a), FASTA

>6KIO_3 Tubulin alpha-1A chain (chains a)
RECISIHVGQAGVQIGNACWELYCLEHGIQPDGHVPRAVFVDLEPTVIDEVRTGTYRQLF
HPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGS
GFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
AIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHF
PLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKD
VNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEA
WARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS

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 P02554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5XP3 2.3 Å, Crystal structure of apo T2R-TTL
6XES 2.32 Å, Tubulin-RB3_SLD in complex with compound 40a
7EMJ 2.33 Å, Crystal structure of T2R-TTL-Barbigerone complex
7XQY 2.35 Å, Crystal structure of T2R-TTL-15 complex
7EXC 2.39 Å, Crystal structure of T2R-TTL-1129A2 complex
6LS4 2.4 Å, A novel anti-tumor agent S-40 in complex with tubulin

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