9F07: Tubulin:stathmin:darpin:tau MTBR3 complex

Tubulin:stathmin:darpin:tau MTBR3 complex. Determined by X-ray diffraction at 2.21 Å resolution. Released 13 Nov 2024.

Method: X-ray diffraction
Resolution: 2.21 Å
Organisms: Ovis aries, Homo sapiens, synthetic construct
Chains: 8
Atoms: 17,447
Mol. weight: 270.17 kDa
Ligands: GDP, MG, GTP
Released: 13 Nov 2024

Explore 9F07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F07 contains 122 α-helices and 78 β-strands across 8 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: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-27	18
β-strand	35	1	2
α-helix	47-51	5
β-strand	53	1	3
β-strand	60	1	2
β-strand	63	1	3
β-strand	65-69	5	1
α-helix	73-78	6
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	253-259	7
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
β-strand	312-321	10	4
α-helix	325-338	14
β-strand	343	1	4
β-strand	349-356	8	4
α-helix	359-360	2
β-strand	368	1	5
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-434	20
β-strand	435	1	6
β-strand	437	1	6

Chain B: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	10-28	19
β-strand	30	1	8
β-strand	36	1	8
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	9
β-strand	60-63	4	9
β-strand	65-69	5	7
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	7
α-helix	103-108	6
α-helix	110-128	19
β-strand	132-140	9	7
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	7
α-helix	183-197	15
β-strand	200-205	6	7
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	267-268	2	7
β-strand	269-273	5	10
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	10
α-helix	307-309	3
β-strand	312-321	10	10
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	10
β-strand	351-356	6	10
α-helix	358-360	3
β-strand	373-381	9	10
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	208-215	8	4
β-strand	218-226	9	4
α-helix	248-290	43

Chain D: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	148-157	10
α-helix	161-169	9
α-helix	184-191	8
α-helix	194-202	9
α-helix	217-223	7
α-helix	227-235	9
α-helix	250-257	8
α-helix	260-268	9
α-helix	283-291	9
β-strand	306-311	6	11

Chain E: 25 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
α-helix	10-28	19
β-strand	35	1	13
α-helix	48-51	4
β-strand	53-55	3	14
β-strand	60	1	13
β-strand	61-63	3	14
β-strand	65-69	5	12
α-helix	73-78	6
α-helix	89-91	3
β-strand	92-94	3	12
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	134-140	7	12
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	12
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	12
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	15
β-strand	277	1	16
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	15
β-strand	312-321	10	15
α-helix	325-338	14
β-strand	343	1	15
β-strand	349-356	8	15
α-helix	359-360	2
β-strand	368	1	16
α-helix	369-370	2
β-strand	373-381	9	15
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-434	20

Chain F: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-27	18
β-strand	30	1	17
β-strand	36	1	17
α-helix	41-43	3
α-helix	49-51	3
β-strand	53-56	4	18
β-strand	60-63	4	18
β-strand	65-69	5	11
α-helix	74-79	6
α-helix	89-91	3
β-strand	92-94	3	11
α-helix	103-108	6
α-helix	110-128	19
β-strand	132-140	9	11
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	11
α-helix	183-197	15
β-strand	200-205	6	11
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	11
β-strand	269-273	5	19
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	19
α-helix	307-309	3
β-strand	312-321	10	19
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	19
β-strand	351-356	6	19
α-helix	358-360	3
β-strand	373-381	9	19
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain G: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	208-215	8	15
β-strand	218-226	9	15
α-helix	248-290	43
β-strand	307-312	6	11
α-helix	313-314	2

Chain H: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	148-157	10
α-helix	161-169	9
α-helix	184-191	8
α-helix	194-202	9
α-helix	217-223	7
α-helix	227-235	9
α-helix	250-257	8
α-helix	260-268	9
α-helix	283-291	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, E	protein	451	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, F	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Stathmin-4	C, G	protein	121	Homo sapiens	Q9H169 (AlphaFold model)
D2-R3	D, H	protein	190	synthetic construct

Sequence of entity 1 (A, E), FASTA

>9F07_1 Tubulin alpha chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, F), FASTA

>9F07_2 Tubulin beta chain (chains B, F)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (C, G), FASTA

>9F07_3 Stathmin-4 (chains C, G)
MADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
AHFAAMLERLQEKDKHAEEVRKNKELKEGGGGSGGGGSGGGSVQIVYKPVDLSKVTSKSG
S

Sequence of entity 4 (D, H), FASTA

>9F07_4 D2-R3 (chains D, H)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNAEDDSGKTPLHLAAIKGHL
EIVEVLLKHGADVNAADKMGDTPLHLAALYGHLEIVEVLLKNGADVNATDTYGFTPLHLA
ADAGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGGGGGSGGGGSGGGSVQIVYKPVD
LSKVTSKSGS

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Water and common crystallization additives (PEG, GOL, PGE, P6G, 1PE) are not listed.

Primary citation

The structure of a Tau fragment bound to tubulin prompts new hypotheses on Tau mechanism and oligomerization. Ammar Khodja, L., Campanacci, V., Lippens, G. et al. PNAS Nexus (2024) 3:pgae487-pgae487. DOI 10.1093/pnasnexus/pgae487 · PubMed

Other PDB entries of the same protein (UniProt D0VWZ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EYP 1.9 Å, Tubulin-darpin complex
3RYC 2.1 Å, Tubulin: RB3 stathmin-like domain complex
4DRX 2.22 Å, GTP-Tubulin in complex with a DARPIN
6TDE 2.29 Å, Tubulin-inhibitor complex
3RYI 2.4 Å, GDP-Tubulin: rb3 stathmin-like domain complex
5KX5 2.5 Å, Crystal structure of tubulin-stathmin-TTL-Compound 11 complex
3RYF 2.52 Å, GTP-Tubulin: RB3 Stathmin-like domain complex
4F6R 2.64 Å, Tubulin:Stathmin-like domain complex
6GVN 2.69 Å, Tubulin:TM-3 DARPin complex
3UT5 2.73 Å, Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex
6H9B 2.75 Å, 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin…
3RYH 2.8 Å, GMPCPP-Tubulin: RB3 Stathmin-like domain complex

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