6VPO: Tubulin alpha-1A chain

Cryo-EM structure of microtubule-bound KLP61F motor domain in the AMPPNP 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: 9,266
Mol. weight: 144.15 kDa
Ligands: GTP, MG, GDP, ANP
Released: 19 Feb 2020

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

Secondary structure: helices and β-sheets

6VPO contains 60 α-helices and 53 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: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
β-strand	35	1	2
β-strand	53-56	4	2
β-strand	60-63	4	2
β-strand	67-69	3	1
α-helix	76-79	4
β-strand	93-94	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-140	9	1
α-helix	145-160	16
β-strand	165-171	7	1
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	1
α-helix	206-213	8
α-helix	224-235	12
α-helix	236-240	5
α-helix	241-243	3
β-strand	248	1	3
α-helix	255-258	4
β-strand	269-271	3	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	312-321	10	3
α-helix	325-337	13
β-strand	343	1	3
β-strand	353-355	3	3
α-helix	359-360	2
α-helix	362-363	2
β-strand	373-381	9	3
α-helix	383-401	19
α-helix	405-411	7
α-helix	416-437	22

Chain B: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	4
α-helix	11-28	18
β-strand	30	1	5
β-strand	36	1	5
α-helix	41-44	4
α-helix	49-51	3
β-strand	53-56	4	6
β-strand	60-63	4	6
β-strand	65-69	5	4
α-helix	72-80	9
α-helix	89-91	3
β-strand	92-94	3	4
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-128	19
β-strand	132-140	9	4
α-helix	144-160	17
β-strand	165-172	8	4
α-helix	173-174	2
α-helix	184-197	14
β-strand	200-205	6	4
α-helix	206-215	10
α-helix	224-243	20
β-strand	246	1	7
α-helix	252-259	8
β-strand	267-268	2	4
β-strand	269-272	4	7
α-helix	289-296	8
α-helix	298-300	3
β-strand	312-320	9	7
α-helix	325-338	14
β-strand	343	1	7
β-strand	351-356	6	7
α-helix	358-360	3
β-strand	374-381	8	7
α-helix	384-400	17
α-helix	406-409	4
α-helix	415-436	22

Chain C: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	19-20	2
β-strand	21-26	6	8
α-helix	27-29	3
α-helix	31-35	5
α-helix	38-39	2
β-strand	40	1	9
β-strand	42-43	2	10
β-strand	50-54	5	10
β-strand	61-65	5	10
β-strand	69-70	2	8
α-helix	76-79	4
α-helix	80-84	5
α-helix	85-89	5
α-helix	90-93	4
β-strand	96-101	6	8
β-strand	104	1	11
α-helix	109-113	5
α-helix	133-148	16
β-strand	151-156	6	8
β-strand	159-161	3	8
β-strand	166-168	3	8
β-strand	180-182	3	12
β-strand	190-192	3	12
β-strand	199-200	2	8
α-helix	203-216	14
β-strand	219-220	2	13
β-strand	228-229	2	13
β-strand	232-242	11	8
β-strand	253-261	9	8
α-helix	262-264	3
β-strand	265	1	11
α-helix	268-271	4
α-helix	277-300	24
α-helix	308-310	3
α-helix	312-316	5
β-strand	325-333	9	8
β-strand	336	1	9
α-helix	340-352	13
α-helix	353-355	3

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

>6VPO_1 Tubulin alpha-1A chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>6VPO_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (C), FASTA

>6VPO_3 Kinesin-like protein Klp61F (chains C)
MDISGGNTSRQPQKKSNQNIQVYVRVRPLNSRERCIRSAEVVDVVGPREVVTRHTLDSKL
TKKFTFDRSFGPESKQCDVYSVVVSPLIEEVLNGYNCTVFAYGQTGTGKTHTMVGNETAE
LKSSWEDDSDIGIIPRALSHLFDELRMMEVEYTMRISYLELYNEELCDLLSTDDTTKIRI
FDDSTKKGSVIIQGLEEIPVHSKDDVYKLLEKGKERRKTATTLMNAQSSRSHTVFSIVVH
IRENGIEGEDMLKIGKLNLVDLAGSENVSKAGNEKGIRVRETVNINQSLLTLGRVITALV
DRAPHVPYRESKLTRLLQESLGGRTKTSIIATISPGHKDIEETLSTLEYAHRAKNIQNKP
EVNQKLTKKLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 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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