6TIW: Human kinesin-5 motor domain in the GSK state

Human kinesin-5 motor domain in the GSK state bound to microtubules (Conformation 2). Determined by electron microscopy at 3.8 Å resolution. Released 4 Mar 2020.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 3
Atoms: 9,491
Mol. weight: 142 kDa
Ligands: MG, G2P, MZK
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6TIW contains 54 α-helices and 44 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	9
α-helix	10-28	19
α-helix	47-52	6
β-strand	53-56	4	10
β-strand	60-63	4	10
β-strand	65-67	3	9
α-helix	72-80	9
α-helix	82-86	5
β-strand	92	1	9
α-helix	103-105	3
α-helix	106-110	5
α-helix	111-128	18
β-strand	134-138	5	9
α-helix	144-161	18
β-strand	165-169	5	9
β-strand	172	1	11
α-helix	173-174	2
α-helix	182-197	16
β-strand	202	1	9
β-strand	205	1	11
α-helix	206-217	12
α-helix	224-243	20
β-strand	248	1	12
α-helix	252-259	8
β-strand	269-273	5	13
α-helix	278-283	6
α-helix	288-296	9
β-strand	312	1	14
α-helix	325-337	13
β-strand	343	1	14
β-strand	355	1	12
α-helix	359-361	3
α-helix	369-370	2
β-strand	375-379	5	13
α-helix	382-401	20
α-helix	405-410	6
α-helix	415-436	22

Chain B: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	5
α-helix	10-28	19
α-helix	41-50	10
β-strand	52-54	3	6
β-strand	58-60	3	6
β-strand	63-65	3	5
α-helix	70-78	9
α-helix	101-126	26
β-strand	133-138	6	5
α-helix	142-158	17
β-strand	165-170	6	5
α-helix	171-172	2
α-helix	180-195	16
β-strand	198-203	6	5
α-helix	204-215	12
α-helix	222-241	20
β-strand	246	1	7
α-helix	250-257	8
β-strand	267-270	4	8
α-helix	276-281	6
α-helix	286-294	9
α-helix	296-298	3
β-strand	314-317	4	7
α-helix	323-336	14
β-strand	350-353	4	7
α-helix	357-358	2
β-strand	366-369	4	8
α-helix	372-391	20
α-helix	395-401	7
α-helix	405-427	23

Chain K: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	20-25	6	1
α-helix	26-29	4
α-helix	30-35	6
β-strand	39	1	2
β-strand	42-44	3	3
β-strand	49-53	5	3
β-strand	63-67	5	3
β-strand	70-72	3	1
α-helix	78-95	18
β-strand	98-105	8	1
α-helix	107-111	5
α-helix	112-116	5
α-helix	136-150	15
β-strand	153-164	12	1
β-strand	167-170	4	1
β-strand	183-187	5	4
β-strand	190-197	8	4
β-strand	202-204	3	1
α-helix	207-221	15
β-strand	236-247	12	1
β-strand	255-265	11	1
α-helix	272-275	4
α-helix	279-304	26
α-helix	311-313	3
α-helix	315-319	5
α-helix	321-323	3
β-strand	329-336	8	1
β-strand	339	1	2
α-helix	343-358	16
α-helix	360-361	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF11	K	protein	391	Homo sapiens	P52732 (AlphaFold model)
Tubulin beta chain	B	protein	429	Sus scrofa	P02554 (AlphaFold model)
Tubulin alpha-1B chain	A	protein	438	Sus scrofa	Q2XVP4 (AlphaFold model)

Sequence of entity 1 (K), FASTA

>6TIW_1 Kinesin-like protein KIF11 (chains K)
MHHHHHHSSGVDLGTENLYFQSMASQPNSSAKKKEEKGKNIQVVVRCRPFNLAERKASAH
SIVECDPVRKEVSVRTGGLADKSSRKTYTFDMVFGASTKQIDVYRSVVCPILDEVIMGYN
CTIFAYGQTGTGKTFTMEGERSPNEEYTWEEDPLAGIIPRTLHQIFEKLTDNGTEFSVKV
SLLEIYNEELFDLLNPSSDVSERLQMFDDPRNKRGVIIKGLEEITVHNKDEVYQILEKGA
AKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDGEELVKIGKLNLVDLAGSENIGRSGAV
DKRAREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISP
ASLNLEETLSTLEYAHRAKNILNKPEVNQKL

Sequence of entity 2 (B), FASTA

>6TIW_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDAT

Sequence of entity 3 (A), FASTA

>6TIW_3 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	2
MZK	6-[4-(trifluoromethyl)phenyl]-3,4-dihydro-1~{H}-quinolin-2-one	C16 H12 F3 N O	1

Primary citation

Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy. Pena, A., Sweeney, A., Cook, A.D. et al. Structure (2020) 28:450-457.e5. DOI 10.1016/j.str.2020.01.013 · PubMed

Other PDB entries of the same protein (UniProt P52732 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZCW 1.69 Å, Eg5 - New allosteric binding site
6TLE 1.75 Å, Human Eg5 motor domain mutant E344K
1X88 1.8 Å, Human Eg5 motor domain bound to Mg-ADP and monastrol
6G6Y 1.8 Å, Eg5-inhibitor complex
2PG2 1.85 Å, Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15
1Q0B 1.9 Å, Crystal structure of the motor protein KSP in complex with ADP and monastrol
2X7C 1.9 Å, Crystal structure of human kinesin Eg5 in complex with (S)-enastron
8YHH 1.95 Å, The Crystal Structure of Mitotic Kinesin Eg5 from Biortus
3K5E 1.97 Å, The structure of human kinesin-like motor protein Kif11/KSP/Eg5 in complex with ADP and…
2WOG 2.0 Å, Intermediate and final states of human kinesin Eg5 in complex with S-trityl-L-cysteine
3L9H 2.0 Å, X-ray structure of mitotic kinesin-5 (KSP, KIF11, Eg5)in complex with the…
5JV3 2.01 Å, The neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1

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