6QVE: Tubulin alpha-1B chain

NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule. Determined by electron microscopy at 3.7 Å resolution. Released 27 Nov 2019.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Naegleria gruberi
Chains: 5
Atoms: 14,591
Mol. weight: 224.41 kDa
Ligands: TA1, GDP, MG, GTP
Released: 27 Nov 2019

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

Secondary structure: helices and β-sheets

6QVE contains 86 α-helices and 83 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: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	5
α-helix	12-26	15
α-helix	49-51	3
β-strand	55	1	6
β-strand	61	1	6
β-strand	65-66	2	5
β-strand	68	1	7
α-helix	75-80	6
β-strand	93	1	7
α-helix	103-105	3
α-helix	115-123	9
β-strand	132-140	9	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	173-174	2
α-helix	188-194	7
β-strand	200-205	6	5
α-helix	207-214	8
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-254	3
α-helix	255-258	4
α-helix	268	1
β-strand	269-273	5	5
α-helix	288-291	4
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-314	3	8
β-strand	317-321	5	5
α-helix	325-335	11
β-strand	353-355	3	5
α-helix	361-363	3
β-strand	373-379	7	5
β-strand	380-381	2	8
α-helix	385-396	12
α-helix	406-409	4
α-helix	416-436	21

Chain C: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	12-26	15
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-68	4	1
α-helix	73-78	6
β-strand	93	1	1
α-helix	103-105	3
α-helix	115-123	9
α-helix	126-128	3
β-strand	132-140	9	1
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-205	6	1
α-helix	206-214	9
α-helix	229-238	10
β-strand	248	1	3
β-strand	269-273	5	1
α-helix	279-281	3
α-helix	291-295	5
α-helix	307-309	3
β-strand	312-316	5	1
β-strand	317-318	2	4
β-strand	319-321	3	1
α-helix	325-335	11
β-strand	343	1	1
β-strand	353-354	2	4
β-strand	355	1	3
α-helix	359-363	5
α-helix	368-370	3
β-strand	373-381	9	1
α-helix	385-388	4
α-helix	390-399	10
α-helix	405-408	4
α-helix	409-411	3
α-helix	420-436	17

Chain G: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	17
α-helix	10-27	18
β-strand	30	1	18
β-strand	36	1	18
α-helix	44-51	6
β-strand	53-56	4	19
β-strand	60-63	4	19
β-strand	65-68	4	17
α-helix	72-80	9
β-strand	92-93	2	17
α-helix	115-126	12
β-strand	132-138	7	17
β-strand	140	1	20
α-helix	154-157	4
β-strand	165-168	4	17
β-strand	171-172	2	20
α-helix	183-194	12
β-strand	200-202	3	17
β-strand	204-205	2	20
α-helix	207-211	5
α-helix	212-216	5
α-helix	224-235	12
β-strand	246-248	3	21
α-helix	254-257	4
β-strand	267-268	2	17
β-strand	272-273	2	21
α-helix	280-282	3
α-helix	290-293	4
α-helix	298-300	3
β-strand	312	1	22
β-strand	315-321	7	21
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	22
β-strand	351-356	6	21
β-strand	373-378	6	21
β-strand	381	1	22
α-helix	385-400	16
α-helix	405-408	4
α-helix	409-411	3
α-helix	417-434	18

Chain H: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	11-27	17
β-strand	30	1	12
β-strand	36	1	12
α-helix	44-51	6
β-strand	53-56	4	13
β-strand	60-63	4	13
β-strand	65-69	5	11
α-helix	72-80	9
β-strand	93-94	2	11
α-helix	116-126	11
β-strand	132-138	7	11
α-helix	145-148	4
α-helix	154-160	7
β-strand	165-168	4	11
β-strand	171	1	14
α-helix	172-174	3
α-helix	183-186	4
α-helix	188-197	10
β-strand	200-202	3	11
β-strand	204	1	14
α-helix	207-214	8
α-helix	224-238	15
α-helix	239-241	3
β-strand	246-248	3	15
α-helix	254-257	4
β-strand	267-268	2	11
β-strand	269-273	5	15
α-helix	288-293	6
α-helix	298-300	3
β-strand	312	1	16
β-strand	315-319	5	15
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	16
β-strand	351-356	6	15
β-strand	375-379	5	15
β-strand	381	1	16
α-helix	385-400	16
α-helix	409-411	3
α-helix	415-434	20

Chain W: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	636-642	7
α-helix	643-647	5
α-helix	654-657	4
α-helix	659-662	4
β-strand	672	1	9
β-strand	675-677	3	10
β-strand	685-690	6	10
β-strand	691	1	9
β-strand	733-736	4	10
β-strand	748-755	8	10
β-strand	760-763	4	10
β-strand	775-778	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Homo sapiens	P68363 (AlphaFold model)
Predicted protein	W	protein	187	Naegleria gruberi	D2VJG4 (AlphaFold model)
Beta1-tubulin	G, H	protein	444	Homo sapiens	P07437 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6QVE_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (W), FASTA

>6QVE_2 Predicted protein (chains W)
MAHHHHHHSAALEVLFQGPNGMILKNMKQPNKTNKLLIKNALIHLTLAGEVNKKEREDVF
EAMKEYEDTNQMIILVREVNVPAFRALYVVVTDGLNANVGSSTSTTDSNRTDNSSRSESP
NIEKRSDQILVKKIIGKGPKFLTEDVVDVFCRYDSGGKKLSKLSSRTFGVTTDVVVLKSA
AIKKIKR

Sequence of entity 3 (G, H), FASTA

>6QVE_3 Beta1-tubulin (chains G, H)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Ligands and cofactors

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