6VZR: Engineered TTLL6

Engineered TTLL6 bound to the initiation analog. Determined by X-ray diffraction at 2.6 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Mus musculus
Chains: 6
Atoms: 13,457
Mol. weight: 221.51 kDa
Ligands: 2TI, ADP, MG
Released: 12 Aug 2020

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

Secondary structure: helices and β-sheets

6VZR contains 78 α-helices and 80 β-strands across 6 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-66	6	1
α-helix	70-79	10
β-strand	82-83	2	1
β-strand	92-95	4	1
α-helix	101-104	4
β-strand	112-113	2	1
α-helix	120-123	4
α-helix	125-138	14
β-strand	149-152	4	2
α-helix	156-165	10
β-strand	171-174	4	2
β-strand	185-187	3	2
α-helix	190-192	3
β-strand	199-203	5	2
β-strand	208	1	3
β-strand	210-211	2	4
β-strand	214-215	2	4
β-strand	216-227	12	5
β-strand	230-235	6	5
β-strand	239-242	4	5
α-helix	243	1
α-helix	258-261	4
α-helix	265-268	4
β-strand	283-285	3	5
α-helix	286-295	10
α-helix	300-317	18
α-helix	319-329	11
β-strand	339	1	1
β-strand	341-349	9	5
β-strand	350	1	3
α-helix	354	1
β-strand	355-361	7	5
α-helix	371-387	17
α-helix	390-392	3
α-helix	395-410	16
α-helix	417-437	21
β-strand	444-448	5	5
α-helix	453-459	7

Chain B: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-66	6	6
α-helix	70-79	10
β-strand	82-83	2	6
β-strand	92-95	4	6
α-helix	101-104	4
β-strand	112-113	2	6
α-helix	120-123	4
α-helix	125-138	14
β-strand	149-152	4	7
α-helix	156-165	10
β-strand	171-174	4	7
β-strand	185-187	3	7
α-helix	190-192	3
β-strand	199-203	5	7
β-strand	208	1	8
β-strand	210-211	2	9
β-strand	214-215	2	9
β-strand	216-227	12	10
β-strand	230-235	6	10
β-strand	239-242	4	10
α-helix	243	1
α-helix	258-261	4
α-helix	265-268	4
β-strand	283-285	3	10
α-helix	286-295	10
α-helix	300-317	18
α-helix	319-329	11
β-strand	339	1	6
β-strand	341-349	9	10
β-strand	350	1	8
α-helix	354	1
β-strand	355-361	7	10
α-helix	371-387	17
α-helix	390-392	3
α-helix	395-410	16
α-helix	415-437	23
β-strand	444-448	5	10
α-helix	453-459	7

Chain C: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-66	6	11
α-helix	70-79	10
β-strand	82-83	2	11
β-strand	92-95	4	11
α-helix	101-105	5
β-strand	112-113	2	11
α-helix	120-123	4
α-helix	125-138	14
β-strand	149-152	4	12
α-helix	156-165	10
β-strand	171-174	4	12
β-strand	185-187	3	12
α-helix	190-192	3
β-strand	199-203	5	12
β-strand	208	1	13
β-strand	210-211	2	14
β-strand	214-215	2	14
β-strand	216-227	12	15
β-strand	230-235	6	15
β-strand	239-242	4	15
α-helix	243	1
α-helix	258-261	4
α-helix	265-268	4
β-strand	283-285	3	15
α-helix	286-295	10
α-helix	300-317	18
α-helix	319-329	11
β-strand	339	1	11
β-strand	341-349	9	15
β-strand	350	1	13
α-helix	354	1
β-strand	355-361	7	15
α-helix	371-387	17
α-helix	390-392	3
α-helix	395-410	16
α-helix	415-440	26
β-strand	444-448	5	15
α-helix	453-459	7

Chain D: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-66	6	16
α-helix	70-79	10
β-strand	82-83	2	16
β-strand	92-95	4	16
α-helix	101-105	5
β-strand	112-113	2	16
α-helix	120-123	4
α-helix	125-138	14
β-strand	149-152	4	17
α-helix	156-165	10
β-strand	171-174	4	17
β-strand	185-187	3	17
α-helix	190-192	3
β-strand	199-203	5	17
β-strand	208	1	18
β-strand	210-211	2	19
β-strand	214-215	2	19
β-strand	216-227	12	20
β-strand	230-235	6	20
β-strand	239-242	4	20
α-helix	243	1
α-helix	258-261	4
α-helix	265-268	4
β-strand	283-285	3	20
α-helix	286-295	10
α-helix	300-317	18
α-helix	319-329	11
β-strand	339	1	16
β-strand	341-349	9	20
β-strand	350	1	18
α-helix	354	1
β-strand	355-361	7	20
α-helix	371-387	17
α-helix	390-392	3
α-helix	395-410	16
α-helix	415-437	23
β-strand	444-448	5	20
α-helix	453-459	7

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-16	9

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin polyglutamylase TTLL6	A, B, C, D	protein	453	Mus musculus	A4Q9E8 (AlphaFold model)
TTLL6 unregistered chain	F	protein	12	Mus musculus
TTLL6 unregistered chain	G	protein	11	Mus musculus

Sequence of entity 1 (A, B, C, D), FASTA

>6VZR_1 Tubulin polyglutamylase TTLL6 (chains A, B, C, D)
GKKKRKKKRLVINLSNCRYDSVRRAAQQYGLREAGDNDDWTLYWTDYSVSLERVMEMKSY
QKINHFPGMSEICRKDLLARNMSRMLKLFPKDFHFFPRTWCLPADWGDLQTYSRTRKNKT
YICKPDSGARGRGIFITRSVKEIKPGEDMICQLYISKPFIIDGFKFDLRVYVLVTSCDPL
RVFVYNEGLARFATTSYSHPNLDNLDEICMHLTNYSINKHSSNFVQDAFSGSKRKLSTFN
SYMKTHGYDVEQIWRGIEDVIIKTLISAHPVIKHNYHTCFPSHTLNSACFEILGFDILLD
RKLKPWLLEVNISPSFSTDSKLDKEVKDSLLYDALVLINLGNCDKKKVLEEERQRGRFLQ
QCPNREIRLEEVKGFQAMRLQKTEEYEKKNCGGFRLIYPGLNLEKYDKFFQDNSSLFQNT
VASRARELYARQLIQELRQKQEKKVFLKKARKE

Sequence of entity 2 (F), FASTA

>6VZR_2 TTLL6 unregistered chain (chains F)
XXXXXXXXXXXX

Sequence of entity 3 (G), FASTA

>6VZR_3 TTLL6 unregistered chain (chains G)
XXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
2TI	(2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphon…	C14 H26 N2 O11 P2	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
MG	Magnesium ion	Mg	8

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes. Mahalingan, K.K., Keith Keenan, E., Strickland, M. et al. Nat Struct Mol Biol (2020) 27:802-813. DOI 10.1038/s41594-020-0462-0 · PubMed

Other PDB entries of the same protein (UniProt A4Q9E8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VZU 1.98 Å, TTLL6 bound to alpha-elongation analog
6VZT 2.18 Å, TTLL6 bound to ATP
6VZV 2.33 Å, TTLL6 bound to gamma-elongation analog
6VZW 2.5 Å, TTLL6 bound to the initiation analog
6VZS 2.66 Å, Engineered TTLL6 mutant bound to gamma-elongation analog
6VZQ 3.08 Å, Engineered TTLL6 mutant bound to alpha-elongation analog
8T42 3.6 Å, Model of TTLL6 MTBH1-2 bound to microtubule
8U3Z 3.6 Å, Model of TTLL6 bound to microtubule from composite map

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