6QUY: Tubulin alpha-1B chain

NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule. Determined by electron microscopy at 3.8 Å resolution. Released 27 Nov 2019.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Naegleria gruberi
Chains: 5
Atoms: 14,637
Mol. weight: 224.41 kDa
Ligands: GTP, MG, GDP, TA1
Released: 27 Nov 2019

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

Secondary structure: helices and β-sheets

6QUY contains 87 α-helices and 82 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: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
α-helix	10-26	17
β-strand	55	1	2
β-strand	61	1	2
β-strand	65-66	2	1
β-strand	67-68	2	3
α-helix	73-79	7
β-strand	92-93	2	3
α-helix	103-105	3
α-helix	115-125	11
β-strand	132-140	9	1
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	173-174	2
α-helix	188-194	7
β-strand	200-205	6	1
α-helix	207-214	8
α-helix	224-238	15
β-strand	246	1	4
α-helix	255-259	5
β-strand	269-273	5	1
α-helix	290-293	4
α-helix	298-300	3
β-strand	312-314	3	5
β-strand	317-321	5	1
α-helix	325-335	11
β-strand	343	1	5
β-strand	353-355	3	1
β-strand	356	1	4
α-helix	359-363	5
β-strand	373-379	7	1
β-strand	380-381	2	5
α-helix	385-400	16
α-helix	406-409	4
α-helix	417-436	20

Chain C: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-26	17
β-strand	53	1	7
β-strand	63	1	7
β-strand	65-68	4	6
α-helix	73-78	6
β-strand	93	1	6
α-helix	103-105	3
α-helix	115-123	9
β-strand	132-140	9	6
α-helix	150-160	11
β-strand	165-172	8	6
α-helix	173-174	2
α-helix	188-194	7
β-strand	200-205	6	6
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
α-helix	254-258	5
β-strand	269	1	6
β-strand	272-273	2	8
α-helix	279-281	3
α-helix	290-295	6
α-helix	298-300	3
β-strand	312-314	3	9
β-strand	317	1	10
β-strand	320-321	2	11
α-helix	325-335	11
β-strand	343	1	9
β-strand	353	1	10
α-helix	358-363	6
β-strand	373-374	2	11
β-strand	375-376	2	8
β-strand	379	1	6
β-strand	380-381	2	9
α-helix	385-396	12
α-helix	406-409	4
α-helix	417-419	3
α-helix	421-436	16

Chain G: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	19
α-helix	10-27	18
β-strand	30	1	20
β-strand	36	1	20
α-helix	41-44	4
α-helix	49-51	3
β-strand	53-55	3	21
α-helix	57-59	3
β-strand	61-63	3	21
β-strand	65-67	3	19
β-strand	68-69	2	22
α-helix	73-80	8
β-strand	93-94	2	22
α-helix	105-109	5
α-helix	116-128	13
β-strand	132-139	8	19
α-helix	145-148	4
α-helix	150-157	8
β-strand	165-171	7	19
α-helix	172-174	3
α-helix	183-186	4
α-helix	188-191	4
β-strand	200-204	5	19
α-helix	207-211	5
α-helix	212-216	5
α-helix	224-238	15
α-helix	239-241	3
β-strand	248	1	23
α-helix	254-257	4
β-strand	267-268	2	19
β-strand	269-273	5	23
α-helix	280-283	4
α-helix	288-295	8
β-strand	312	1	24
β-strand	315-320	6	23
α-helix	325-338	14
β-strand	351-355	5	23
β-strand	374-379	6	23
β-strand	381	1	24
α-helix	385-400	16
α-helix	406-409	4
α-helix	417-434	18

Chain H: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	13
α-helix	10-27	18
β-strand	30	1	14
β-strand	36	1	14
α-helix	44-51	6
β-strand	53-55	3	15
α-helix	57-59	3
β-strand	61-63	3	15
β-strand	65-69	5	13
α-helix	73-80	8
β-strand	92-94	3	13
α-helix	103-104	2
α-helix	105-109	5
α-helix	116-128	13
β-strand	132-139	8	13
α-helix	145-148	4
α-helix	150-160	11
β-strand	165-171	7	13
α-helix	172-174	3
α-helix	183-186	4
α-helix	188-194	7
β-strand	200-204	5	13
α-helix	207-211	5
α-helix	212-216	5
α-helix	224-226	3
α-helix	228-239	12
β-strand	248	1	16
α-helix	254-257	4
β-strand	267-268	2	13
β-strand	269-273	5	17
α-helix	280-282	3
α-helix	288-295	8
β-strand	312	1	18
β-strand	315-319	5	17
α-helix	325-338	14
β-strand	343	1	18
β-strand	351-354	4	17
β-strand	355	1	16
β-strand	375-379	5	17
β-strand	381	1	18
α-helix	385-400	16
α-helix	406-409	4
α-helix	417-431	15

Chain W: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	636-642	7
α-helix	643-647	5
α-helix	654-661	8
β-strand	672-677	6	12
β-strand	685-691	7	12
β-strand	734	1	12
β-strand	750-754	5	12
β-strand	761-763	3	12
β-strand	775-777	3	12
α-helix	780-782	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Homo sapiens	P68363 (AlphaFold model)
CKK domain protein	W	protein	187	Naegleria gruberi	D2VJG4 (AlphaFold model)
Tubulin beta chain	G, H	protein	444	Homo sapiens	P07437 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6QUY_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (W), FASTA

>6QUY_2 CKK domain protein (chains W)
MAHHHHHHSAALEVLFQGPNGMILKNMKQPNKTNKLLIKNALIHLTLAGEVNKKEREDVF
EAMKEYEDTNQMIILVREVNVPAFRALYVVVTDGLNANVGSSTSTTDSNRTDNSSRSESP
NIEKRSDQILVKKIIGKGPKFLTEDVVDVFCRYDSGGKKLSKLSSRTFGVTTDVVVLKSA
AIKKIKR

Sequence of entity 3 (G, H), FASTA

>6QUY_3 Tubulin beta chain (chains G, H)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
TA1	Taxol	C47 H51 N O14	2

Primary citation

Structural determinants of microtubule minus end preference in CAMSAP CKK domains. Atherton, J., Luo, Y., Xiang, S. et al. Nat Commun (2019) 10:5236-5236. DOI 10.1038/s41467-019-13247-6 · PubMed

Other PDB entries of the same protein (UniProt P68363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8L 1.8 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule

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