6MZE: Tubulin alpha-1A chain

Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with Tumor Overexpressed Gene (TOG) Domain Arrays. Determined by X-ray diffraction at 3.6 Å resolution. Released 28 Nov 2018.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Sus scrofa, Lachancea kluyveri NRRL Y-12651, Escherichia coli
Chains: 28
Atoms: 77,878
Mol. weight: 1196.46 kDa
Ligands: GDP, MG, GTP
Released: 28 Nov 2018

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

Secondary structure: helices and β-sheets

6MZE contains 629 α-helices and 288 β-strands across 28 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
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-69	10
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-165	7

Chains A and O: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	72-78	7
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-140	9	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	183-193	11
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	3
β-strand	277	1	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-338	14
β-strand	343	1	3
α-helix	351	1
β-strand	352-356	5	3
β-strand	368	1	4
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Chains b, F, G, M, T and U: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-165	7

Chains B and P: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	41-46	4
β-strand	53	1	7
β-strand	63	1	7
β-strand	65-69	5	5
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	183-197	15
β-strand	200-205	6	5
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	5
β-strand	269	1	8
β-strand	271	1	9
β-strand	272-273	2	8
α-helix	285-287	3
α-helix	288-292	5
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-320	9	8
α-helix	325-337	13
α-helix	340-342	3
β-strand	343	1	8
β-strand	351-356	6	8
α-helix	359-360	2
β-strand	374-381	8	8
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	415-436	22

Chains C, J and X: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-69	5	10
α-helix	72-78	7
α-helix	89-91	3
β-strand	92-94	3	10
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	134-140	7	10
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	183-193	11
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	12
β-strand	277	1	13
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	12
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-338	14
β-strand	343	1	12
α-helix	350-351	2
β-strand	352-356	5	12
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Chains D, R and Y: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-28	19
β-strand	30	1	15
β-strand	36	1	15
α-helix	41-46	4
β-strand	53	1	16
β-strand	63	1	16
β-strand	65-69	5	14
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	14
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-140	9	14
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	14
α-helix	183-197	15
β-strand	200-205	6	14
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	14
β-strand	269	1	17
β-strand	271	1	18
β-strand	272-273	2	17
α-helix	285-287	3
α-helix	288-292	5
α-helix	298-300	3
β-strand	301	1	18
α-helix	307-309	3
β-strand	312-320	9	17
α-helix	325-337	13
α-helix	340-342	3
β-strand	343	1	17
β-strand	351-356	6	17
α-helix	359-360	2
β-strand	374-381	8	17
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	415-436	22

Chain E: 37 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-19	5
α-helix	23-39	17
α-helix	57-63	7
α-helix	68-84	17
α-helix	93-104	12
α-helix	105-109	5
α-helix	114-130	17
α-helix	135-141	7
α-helix	143-146	4
α-helix	150-165	16
α-helix	175-183	9
α-helix	186-190	5
α-helix	195-209	15
α-helix	214-217	4
α-helix	218-222	5
α-helix	227-239	13
α-helix	256-259	4
α-helix	298-301	4
α-helix	302-304	3
α-helix	306-307	2
β-strand	308	1	19
α-helix	311-313	3
α-helix	316-318	3
α-helix	319-322	4
α-helix	327-336	10
α-helix	337-342	6
β-strand	348	1	19
α-helix	359-368	10
α-helix	372-388	17
α-helix	396-408	13
α-helix	414-429	16
α-helix	436-444	9
α-helix	449-464	16
α-helix	475-478	4
α-helix	480-485	6
α-helix	486-492	7
α-helix	497-514	18
α-helix	520-525	6
α-helix	528-540	13

Chain H: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	20
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	21
β-strand	61-63	3	21
β-strand	65-69	5	20
α-helix	72-78	7
α-helix	89-91	3
β-strand	92-94	3	20
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	134-140	7	20
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	20
α-helix	183-193	11
β-strand	200-205	6	20
α-helix	206-215	10
α-helix	224-244	21
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	22
β-strand	277	1	23
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	22
α-helix	307-309	3
β-strand	312-321	10	22
α-helix	325-338	14
β-strand	343	1	22
β-strand	352-356	5	22
β-strand	368	1	23
α-helix	369-370	2
β-strand	373-381	9	22
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

9 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
Tubulin alpha-1A chain	A, C, H, J, O, Q, V, X	protein	451	Sus scrofa	P02550 (AlphaFold model)
Tubulin beta chain	B, D, I, K, P, R, W, Y	protein	445	Sus scrofa	P02554 (AlphaFold model)
Protein Stu2p/Alp14p	E, L, S, Z	protein	536	Lachancea kluyveri NRRL Y-12651	A0A493R6X7 (AlphaFold model)
Designed ankyrin repeat protein (DARPIN) D1	F, G, M, N, T, U, a, b	protein	169	Escherichia coli

Sequence of entity 1 (A, C, H, J, O, Q, V, X), FASTA

>6MZE_1 Tubulin alpha-1A chain (chains A, C, H, J, O, Q, V, X)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D, I, K, P, R, W, Y), FASTA

>6MZE_2 Tubulin beta chain (chains B, D, I, K, P, R, W, Y)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (E, L, S, Z), FASTA

>6MZE_3 Protein Stu2p/Alp14p (chains E, L, S, Z)
MADQDDVDFTTLPLEQRASHKVWKARLNAYQELNNLFTKSSVISPPNDVANYWLDPELFA
SYIVDSNVVAQENAIIALHTLLEYISQVPNVSTSKLRLQWIPPLVEKGLSSSRAATKAKA
TDCIMLLTQSDTSIQQTVNLMLPSLSNKLPRLVSSCVKCLATIIEEFGFINVSDINILLS
EILEPLPKLSSHADRNVRSETMNLILQIYKWFGKELLQELLLEKLKPIQQRDLSRMFEKY
EGTIPPKQQPRLFQWAVPAQSDNNSTLQTDKDGDTLMGNAVDPFELLPPSVILDKFPADF
QTRISSTKWKDRVEALEEIHNNVLKPVKKLAHKNQDYSDYLRVLANVIQKDANVQAVTIA
ANSVQLLCNSLRSNFTRSYGAIVLVPLLERTKEKKPSVNEAICSALDAVATYCGFDDCLE
ETLNYMKHKTPQVRIECTKFLTRMLQGWKSDGPLQNQLLFKLLPEVTTAVLKIVNDTQPT
TRNTGFECFATLMKLVGERELADPLEKLDNLKKKKIYEYYEKVEVATGLEHHHHHH

Sequence of entity 4 (F, G, M, N, T, U, a, b), FASTA

>6MZE_4 Designed ankyrin repeat protein (DARPIN) D1 (chains F, G, M, N, T, U, a, b)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHL
EIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLA
AIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	8
MG	Magnesium ion	Mg	16
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	8

Primary citation

Structural basis of tubulin recruitment and assembly by microtubule polymerases with Tumor Overexpressed Gene (TOG) domain arrays. Nithianantham, S., Cook, B.D., Beans, M. et al. Elife (2018) 7. DOI 10.7554/eLife.38922 · 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
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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