6MLR: Microtubule-bound Kif7 in the AMPPNP state

Cryo-EM structure of microtubule-bound Kif7 in the AMPPNP state. Determined by electron microscopy at 4.2 Å resolution. Released 1 May 2019.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 3
Atoms: 9,177
Mol. weight: 146.02 kDa
Ligands: GDP, ANP, TA1, GTP
Released: 1 May 2019

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

Secondary structure: helices and β-sheets

6MLR contains 57 α-helices and 45 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
α-helix	11-27	17
β-strand	65-67	3	1
β-strand	69	1	2
α-helix	72-78	7
β-strand	94	1	2
α-helix	103-107	5
α-helix	109-128	20
β-strand	135-138	4	1
α-helix	145-161	17
β-strand	166-171	6	1
α-helix	172-174	3
α-helix	183-191	9
α-helix	195-197	3
β-strand	200-204	5	1
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-235	12
α-helix	236-240	5
α-helix	253-258	6
β-strand	269-272	4	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	312	1	4
β-strand	314-321	8	3
α-helix	325-327	3
α-helix	328-332	5
α-helix	333-336	4
β-strand	343	1	4
β-strand	351-355	5	3
β-strand	373-380	8	3
α-helix	384-399	16
α-helix	405-409	5
α-helix	415-434	20

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	41-43	3
α-helix	49-51	3
β-strand	53-54	2	7
β-strand	62-63	2	7
β-strand	65-69	5	5
α-helix	72-79	8
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	132-138	7	5
α-helix	148-160	13
β-strand	165-172	8	5
α-helix	173-174	2
α-helix	185-192	8
β-strand	200-205	6	5
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-242	19
α-helix	252-258	7
β-strand	268	1	5
β-strand	269-272	4	8
α-helix	288-295	8
α-helix	307-309	3
β-strand	312-320	9	8
α-helix	326-338	13
α-helix	340-342	3
β-strand	351-352	2	8
β-strand	355	1	8
β-strand	374-381	8	8
α-helix	385-395	11
α-helix	406-409	4
α-helix	416-436	21

Chain C: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
β-strand	17-22	6	9
α-helix	23-26	4
α-helix	27-30	4
β-strand	36	1	10
β-strand	38-39	2	11
β-strand	46-49	4	11
β-strand	53-56	4	11
β-strand	59-61	3	9
α-helix	62	1
α-helix	67-70	4
α-helix	71-75	5
α-helix	76-82	7
β-strand	88-94	7	9
α-helix	100-104	5
α-helix	119-133	15
β-strand	142-149	8	9
β-strand	152-155	4	9
β-strand	168	1	12
β-strand	178	1	12
β-strand	184-185	2	9
α-helix	189-201	13
β-strand	218-228	11	9
β-strand	243-252	10	9
α-helix	267-286	20
α-helix	301-303	3
α-helix	305-308	4
β-strand	319-326	8	9
β-strand	329	1	10
α-helix	333-344	12

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 KIF7	C	protein	399	Homo sapiens	Q2M1P5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MLR_1 Tubulin alpha-1A chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>6MLR_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (C), FASTA

>6MLR_3 Kinesin-like protein KIF7 (chains C)
GMGLEAQRLPGAEEAPVRVALRVRPLLPKELLHGHQSCLQVEPGLGRVTLGRDRHFGFHV
VLAEDAGQEAVYQACVQPLLEAFFEGFNATVFAYGQTGSGKTYTMGEASVASLLEDEQGI
VPRAMAEAFKLIDENDLLDCLVHVSYLEVYKEEFRDLLEVGTASRDIQLREDERGNVVLC
GVKEVDVEGLDEVLSLLEMGNAARHTGATHLNHLSSRSHTVFTVTLEQRGRAPSRLPRPA
PGQLLVSKFHFVDLAGSERVLKTGSTGERLKESIQINSSLLALGNVISALGDPQRRGSHI
PYRDSKITRILKDSLGGNAKTVMIACVSPSSSDFDETLNTLNYASRAQNIRNRATVNWRP
EAERPPEETASGARGPPRHRSETRIIHRGRRAPGPATAS

Ligands and cofactors

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

Primary citation

Interplay between the Kinesin and Tubulin Mechanochemical Cycles Underlies Microtubule Tip Tracking by the Non-motile Ciliary Kinesin Kif7. Jiang, S., Mani, N., Wilson-Kubalek, E.M. et al. Dev Cell (2019) 49:711-730.e8. DOI 10.1016/j.devcel.2019.04.001 · 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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