8U3Z: Model of TTLL6

Model of TTLL6 bound to microtubule from composite map. Determined by electron microscopy at 3.6 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 17,350
Mol. weight: 297.16 kDa
Ligands: ATP, G2P, MG, GTP
Released: 29 May 2024

Explore 8U3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U3Z contains 106 α-helices and 91 β-strands across 5 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: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	46-51	6
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	72-80	9
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	1
α-helix	172-174	3
α-helix	183-192	10
α-helix	193-197	5
β-strand	200-204	5	1
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-239	16
β-strand	248	1	4
α-helix	252-257	6
β-strand	269-273	5	5
α-helix	278-281	4
α-helix	288-296	9
α-helix	307-309	3
β-strand	312	1	6
β-strand	314-321	8	5
α-helix	325-337	13
β-strand	343	1	6
β-strand	351-354	4	5
β-strand	355	1	4
α-helix	358-361	4
β-strand	373-380	8	5
α-helix	384-399	16
α-helix	405-410	6
α-helix	415-435	21

Chain B: 22 helices, 18 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	41-45	5
α-helix	47-49	3
β-strand	51-53	3	9
α-helix	55-57	3
β-strand	59-61	3	9
β-strand	63-67	5	7
α-helix	70-78	9
α-helix	87-89	3
β-strand	91-92	2	7
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-126	19
β-strand	130-138	9	7
α-helix	143-158	16
β-strand	163-170	8	7
α-helix	171	1
α-helix	181-194	14
β-strand	198-203	6	7
α-helix	204-213	10
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	10
α-helix	250-257	8
β-strand	265-266	2	7
β-strand	267	1	10
β-strand	270-271	2	10
α-helix	286-294	9
β-strand	310-318	9	10
α-helix	324-336	13
α-helix	338-340	3
β-strand	341	1	10
β-strand	349-354	6	10
β-strand	364-371	8	10
α-helix	374-390	17
α-helix	395-401	7
α-helix	405-424	20

Chain E: 25 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-27	18
β-strand	30	1	12
β-strand	36	1	12
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-53	3	13
α-helix	55-57	3
β-strand	59-61	3	13
β-strand	63-67	5	11
α-helix	70-77	8
β-strand	91-92	2	11
α-helix	101-102	2
α-helix	103-107	5
α-helix	112-125	14
β-strand	130-136	7	11
α-helix	142-146	5
α-helix	147-158	12
β-strand	163-170	8	11
α-helix	171	1
α-helix	181-192	12
β-strand	198-203	6	11
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	14
α-helix	250-257	8
β-strand	265-266	2	11
β-strand	267	1	14
β-strand	270-271	2	14
α-helix	277-279	3
α-helix	286-294	9
α-helix	305-307	3
β-strand	310-319	10	14
α-helix	324-336	13
α-helix	338-340	3
β-strand	341	1	14
β-strand	349-354	6	14
β-strand	363-371	9	14
α-helix	374-387	14
α-helix	395-399	5
α-helix	405-425	21

Chain F: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	15
α-helix	10-27	18
β-strand	35	1	16
α-helix	46-50	5
β-strand	53-55	3	17
β-strand	60	1	16
β-strand	61-63	3	17
β-strand	65-68	4	15
α-helix	72-80	9
α-helix	105-109	5
α-helix	111-128	18
β-strand	134-140	7	15
α-helix	145-160	16
β-strand	165-171	7	15
α-helix	172-174	3
α-helix	183-196	14
β-strand	200-204	5	15
α-helix	207-215	9
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	18
α-helix	252-259	8
β-strand	269-270	2	15
β-strand	273	1	15
α-helix	288-296	9
α-helix	307-309	3
β-strand	312-321	10	15
α-helix	325-336	12
β-strand	343	1	15
β-strand	351-354	4	15
β-strand	355	1	18
α-helix	358-361	4
β-strand	373-381	9	15
α-helix	384-398	15
α-helix	405-411	7
α-helix	416-435	20

Chain N: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	61-63	3	19
α-helix	71-79	9
β-strand	82-83	2	19
β-strand	92-93	2	19
α-helix	101-104	4
β-strand	112-113	2	19
α-helix	119-121	3
α-helix	125-138	14
β-strand	149-151	3	20
α-helix	156-165	10
β-strand	171-175	5	20
β-strand	185-187	3	20
β-strand	199-203	5	20
β-strand	208	1	21
β-strand	210-211	2	22
β-strand	214-220	7	22
β-strand	222-227	6	23
β-strand	230-235	6	23
β-strand	239-246	8	22
α-helix	258-261	4
α-helix	265-268	4
β-strand	283-284	2	22
α-helix	286-295	10
α-helix	301-316	16
α-helix	319-329	11
β-strand	341-342	2	23
β-strand	344-349	6	22
β-strand	350	1	21
β-strand	355-361	7	22
α-helix	371-387	17
α-helix	395-410	16
α-helix	415-440	26
β-strand	444-448	5	23
α-helix	453-468	16
α-helix	469-474	6
α-helix	480-498	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, F	protein	451	Homo sapiens	P68363 (AlphaFold model)
Tubulin beta chain	B, E	protein	444	Homo sapiens	P07437 (AlphaFold model)
Tubulin polyglutamylase TTLL6	N	protein	822	Mus musculus	A4Q9E8 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>8U3Z_1 Tubulin alpha-1B chain (chains A, F)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, E), FASTA

>8U3Z_2 Tubulin beta chain (chains B, E)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Sequence of entity 3 (N), FASTA

>8U3Z_3 Tubulin polyglutamylase TTLL6 (chains N)
MLQCLTSESEEGAEEREESSTEDLEELKEFVTLAFVRENTQKRLQNAQQHGKKKRKKKRL
VINLSNCRYDSVRRAAQQYGLREAGDNDDWTLYWTDYSVSLERVMEMKSYQKINHFPGMS
EICRKDLLARNMSRMLKLFPKDFHFFPRTWCLPADWGDLQTYSRTRKNKTYICKPDSGCQ
GRGIFITRSVKEIKPGEDMICQLYISKPFIIDGFKFDLRVYVLVTSCDPLRVFVYNEGLA
RFATTSYSHPNLDNLDEICMHLTNYSINKHSSNFVQDAFSGSKRKLSTFNSYMKTHGYDV
EQIWRGIEDVIIKTLISAHPVIKHNYHTCFPSHTLNSACFEILGFDILLDRKLKPWLLEV
NHSPSFSTDSKLDKEVKDSLLYDALVLINLGNCDKKKVLEEERQRGRFLQQCPNREIRLE
EVKGFQAMRLQKTEEYEKKNCGGFRLIYPGLNLEKYDKFFQDNSSLFQNTVASRARELYA
RQLIQELRQKQEKKVFLKKARKAETQGESAGEQARDKVVRLQRQRQQPKCKTVATCPPKQ
SLHPVTLVSCTSGLLLNIRGLKKGEISESLEQKDTKEAMLIPCKPVSARNYSSVPDLRSA
NPSCFEPEFHVPNAKVKEVKSAFMVNIESTAQPITSVESSRDATAPISTSLESLASMSLS
TSPECSSPESVHMVSYNHKQQKASFHKPMQEKKSKPLMFSKSRHLDLNCTSMKNDINRQY
LMSEILQKVQMKKKRPLFPAPKSQYPTLSKERCPHSRSSSRKKEMNSPSVFVLQASHSRA
ESLNDLLVVATQARLDPRPSRSHSGTTTRDSSTQDPKHTATA

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	2
MG	Magnesium ion	Mg	5
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Structural basis for alpha-tubulin-specific and modification state-dependent glutamylation. Mahalingan, K.K., Grotjahn, D.A., Li, Y. et al. Nat Chem Biol (2024) 20:1493-1504. DOI 10.1038/s41589-024-01599-0 · PubMed

Other PDB entries of the same protein (UniProt P68363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8L 1.8 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule

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