5HNW: Tubulin alpha-1B chain

Structural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the AMPPNP state. Determined by electron microscopy at 6.6 Å resolution. Released 10 Aug 2016.

Method: Electron microscopy
Resolution: 6.6 Å
Organisms: Bos taurus, Drosophila melanogaster, Rattus norvegicus
Chains: 3
Atoms: 9,302
Mol. weight: 143.75 kDa
Ligands: GDP, TA1, ANP, GTP
Released: 10 Aug 2016

Explore 5HNW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HNW contains 53 α-helices and 46 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-26	17
β-strand	65-69	5	1
α-helix	72-80	9
β-strand	92-94	3	1
α-helix	103-107	5
α-helix	109-128	20
β-strand	134-139	6	1
α-helix	144-149	6
α-helix	150-160	11
β-strand	165	1	1
β-strand	167-170	4	1
α-helix	184-194	11
β-strand	200-203	4	1
α-helix	206-215	10
α-helix	224-242	19
α-helix	252-259	8
β-strand	269-271	3	1
β-strand	277	1	2
α-helix	288-291	4
α-helix	293-296	4
β-strand	312-321	10	1
α-helix	325-336	12
β-strand	343	1	1
β-strand	351-355	5	1
β-strand	368	1	2
β-strand	373-381	9	1
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-429	15
α-helix	431-434	4

Chain B: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
β-strand	6-9	4	3
α-helix	12-26	15
β-strand	30	1	4
β-strand	36	1	4
α-helix	49-52	4
β-strand	55	1	5
β-strand	61	1	5
β-strand	65-69	5	3
α-helix	72-78	7
α-helix	83-85	3
α-helix	89-91	3
β-strand	92-94	3	3
α-helix	105-109	5
α-helix	111-126	16
β-strand	134-139	6	3
α-helix	144-148	5
α-helix	149-160	12
β-strand	165-170	6	3
α-helix	184-194	11
β-strand	200-202	3	3
α-helix	206-214	9
α-helix	224-242	19
β-strand	248	1	6
α-helix	252-259	8
β-strand	267-268	2	3
β-strand	269-271	3	6
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	6
α-helix	325-338	14
β-strand	351-356	6	6
β-strand	375-381	7	6
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-436	22

Chain K: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
β-strand	29-31	3	7
α-helix	32-35	4
α-helix	36-39	4
β-strand	48-50	3	8
β-strand	54-56	3	8
β-strand	67-68	2	7
α-helix	74-81	8
α-helix	83-90	8
β-strand	95-100	6	7
α-helix	107-111	5
α-helix	124-134	11
β-strand	142-154	13	7
β-strand	157-160	4	7
β-strand	171-173	3	9
β-strand	179-181	3	9
β-strand	186-189	4	7
α-helix	192-203	12
β-strand	208-209	2	10
β-strand	217-218	2	10
β-strand	221-232	12	7
β-strand	239-247	9	7
α-helix	248-250	3
α-helix	254-257	4
α-helix	265-287	23
α-helix	297-301	5
β-strand	312-318	7	7
α-helix	325-333	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	450	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B	protein	444	Bos taurus	Q6B856 (AlphaFold model)
Protein claret segregational,KINESIN HEAVY CHAIN ISOFORM 5C	K	protein	371	Drosophila melanogaster, Rattus norvegicus	P20480 (AlphaFold model), P56536 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5HNW_1 Tubulin alpha-1B chain (chains A)
RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKH
VPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDR
IRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAV
VEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITAS
LRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQ
MVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPT
VVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
REDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>5HNW_2 Tubulin beta-2B chain (chains B)
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVP
RAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVR
KESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVE
PYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLR
FPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMA
ACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGL
KMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSE
YQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (K), FASTA

>5HNW_3 Protein claret segregational,KINESIN HEAVY CHAIN ISOFORM 5C (chains K)
KEQLFQSNMERKELHNTVMDLRGNIKVMCRFRPLNEAEILRGDKFIPKFKGEETVVIQGK
PYVFDRVLPPNTTQEQVYNACAKQIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPQL
MGIIPRIAHDIFDHIYSMDENLEFAIKVSYFEIYLDKIRDLLDVSKTNLAVHEDKNRVPY
VKGCTERFVSSPEEVMDVIDEGKSNRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLS
GKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGTTHVPYRDSKMTR
ILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFAASVNSCKMTKAKRNRYLNNSVANSS
TQSNNSGSFDK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
TA1	Taxol	C47 H51 N O14	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	2

Primary citation

Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility. Yamagishi, M., Shigematsu, H., Yokoyama, T. et al. Structure (2016) 24:1322-1334. DOI 10.1016/j.str.2016.05.021 · PubMed

Other PDB entries of the same protein (UniProt P81947 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8K 1.52 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
8QL2 1.7 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
6ZWB 1.75 Å, Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
4I4T 1.8 Å, Crystal structure of tubulin-RB3-TTL-Zampanolide complex
5IYZ 1.8 Å, Tubulin-MMAE complex
5NQU 1.8 Å, Tubulin Darpin cryo structure
7YZ3 1.8 Å, Molecular snapshots of drug release from tubulin: Apo state
8QEA 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL3 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL4 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL5 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL6 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…

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