6VPP: Tubulin alpha-1A chain

Cryo-EM structure of microtubule-bound KLP61F motor with tail domain in the nucleotide-free state. Determined by electron microscopy at 4.4 Å resolution. Released 19 Feb 2020.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Sus scrofa, Drosophila melanogaster
Chains: 3
Atoms: 9,156
Mol. weight: 143.65 kDa
Ligands: GDP, MG, GTP
Released: 19 Feb 2020

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

Secondary structure: helices and β-sheets

6VPP contains 54 α-helices and 59 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: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
α-helix	10-27	18
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-80	8
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	112-128	17
β-strand	132-138	7	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-169	5	1
α-helix	170-171	2
β-strand	172	1	3
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-202	3	1
β-strand	203	1	4
β-strand	205	1	3
α-helix	206-215	10
α-helix	224-235	12
α-helix	236-240	5
β-strand	246-248	3	4
α-helix	255-259	5
β-strand	269-272	4	4
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	311-321	11	4
α-helix	325-337	13
β-strand	342-343	2	4
β-strand	351-356	6	4
α-helix	359-363	5
β-strand	364	1	5
β-strand	366	1	5
β-strand	373-381	9	4
α-helix	384-401	18
α-helix	405-407	3
α-helix	415-437	23

Chain B: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-28	19
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	41-47	5
α-helix	49-51	3
β-strand	53-56	4	8
β-strand	60-63	4	8
β-strand	65-69	5	6
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-106	4
α-helix	110-128	19
β-strand	132-140	9	6
α-helix	144-160	17
β-strand	165-172	8	6
α-helix	173-174	2
α-helix	183-197	15
β-strand	201-205	5	6
α-helix	206-215	10
α-helix	224-243	20
β-strand	246	1	9
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-272	4	9
α-helix	288-296	9
β-strand	312-320	9	9
α-helix	325-338	14
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	358-360	3
β-strand	374-381	8	9
α-helix	384-401	18
α-helix	406-411	6
α-helix	415-436	22

Chain C: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	21-22	2	10
β-strand	23-26	4	11
α-helix	27-30	4
α-helix	31-35	5
α-helix	38-40	3
β-strand	42-44	3	12
β-strand	50-52	3	12
β-strand	62	1	12
β-strand	68-70	3	11
α-helix	76-92	17
β-strand	97-101	5	10
β-strand	102	1	13
α-helix	107-113	7
β-strand	115	1	14
β-strand	131	1	14
α-helix	133-147	15
β-strand	153-162	10	10
β-strand	165-168	4	10
β-strand	179-181	3	15
β-strand	191-193	3	15
β-strand	198-199	2	10
α-helix	203-216	14
β-strand	220	1	16
β-strand	228	1	16
β-strand	232-240	9	10
β-strand	254-261	8	10
α-helix	262-265	4
α-helix	268-271	4
α-helix	278-300	23
α-helix	312-316	5
α-helix	318-322	5
β-strand	327-329	3	10
β-strand	331	1	13
β-strand	332-333	2	11
α-helix	340-350	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1A chain	A	protein	451	Sus scrofa	P02550 (AlphaFold model)
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)
Kinesin-like protein Klp61F	C	protein	377	Drosophila melanogaster	P46863 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VPP_1 Tubulin alpha-1A chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>6VPP_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (C), FASTA

>6VPP_3 Kinesin-like protein Klp61F (chains C)
MDISGGNTSRQPQKKSNQNIQVYVRVRPLNSRERCIRSAEVVDVVGPREVVTRHTLDSKL
TKKFTFDRSFGPESKQCDVYSVVVSPLIEEVLNGYNCTVFAYGQTGTGKTHTMVGNETAE
LKSSWEDDSDIGIIPRALSHLFDELRMMEVEYTMRISYLELYNEELCDLLSTDDTTKIRI
FDDSTKKGSVIIQGLEEIPVHSKDDVYKLLEKGKERRKTATTLMNAQSSRSHTVFSIVVH
IRENGIEGEDMLKIGKLNLVDLAGSENVSKAGNEKGIRVRETVNINQSLLTLGRVITALV
DRAPHVPYRESKLTRLLQESLGGRTKTSIIATISPGHKDIEETLSTLEYAHRAKNIQNKP
EVNQKLTKKLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. Bodrug, T., Wilson-Kubalek, E.M., Nithianantham, S. et al. Elife (2020) 9. DOI 10.7554/eLife.51131 · 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…
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

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