PDB-6vzt: TTLL6 bound to ATP

ID or keywords:

Entry

Database: PDB / ID: 6vzt

Title

TTLL6 bound to ATP

Components

TTLL6 unregistered chain
Tubulin polyglutamylase TTLL6

Keywords

LIGASE / TTLL6 / glutamylase / tubulin modification / amino acid ligase

Function / homology

Function and homology information

positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / regulation of cilium beat frequency involved in ciliary motility / 9+0 non-motile cilium / microtubule severing /

Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / microtubule bundle formation ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

Mahalingan, K.K. / Keenen, E.K. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	ZIA NS 003163	United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	ZIA NS 003122	United States

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes.
Authors: Mahalingan, K.K. / Keith Keenan, E. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.

History

Deposition	Feb 28, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vzt.cif.gz	408 KB	Display	PDBx/mmCIF format
PDB format	pdb6vzt.ent.gz	276.6 KB	Display	PDB format
PDBx/mmJSON format	6vzt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/6vzt ftp://data.pdbj.org/pub/pdb/validation_reports/vz/6vzt	HTTPS FTP

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Related structure data

Related structure data	6vzqC 6vzrC 6vzsC 6vzuC 6vzvC 6vzwC 4ylrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5koe-3 4z9d-5 5koe-1 4lh6-d 6vzw-1 5e1z-1 6je8-d 5lwe-2 4azg-2 5koe-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tubulin polyglutamylase TTLL6

B: Tubulin polyglutamylase TTLL6

D: TTLL6 unregistered chain

hetero molecules

110 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tubulin polyglutamylase TTLL6

D: TTLL6 unregistered chain

hetero molecules

defined by author
Evidence: gel filtration
55.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tubulin polyglutamylase TTLL6

hetero molecules

defined by author
54.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.633, 75.515, 115.723
Angle α, β, γ (deg.)	90.000, 90.283, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	GLU	GLU	(chain 'A' and (resid 57 through 63 or (resid 64...	A	A	57 - 83	7 - 33
1	2	ASN	ASN	LYS	LYS	(chain 'A' and (resid 57 through 63 or (resid 64...	A	A	87 - 191	37 - 141
1	3	ILE	ILE	PRO	PRO	(chain 'A' and (resid 57 through 63 or (resid 64...	A	A	193 - 331	143 - 281
1	4	HIS	HIS	PHE	PHE	(chain 'A' and (resid 57 through 63 or (resid 64...	A	A	333 - 408	283 - 358
1	5	ILE	ILE	PHE	PHE	(chain 'A' and (resid 57 through 63 or (resid 64...	A	A	417 - 460	367 - 410
2	1	LYS	LYS	GLU	GLU	(chain 'B' and ((resid 57 through 59 and (name N...	B	B	57 - 83	7 - 33
2	2	ASN	ASN	LYS	LYS	(chain 'B' and ((resid 57 through 59 and (name N...	B	B	87 - 191	37 - 141
2	3	ILE	ILE	PRO	PRO	(chain 'B' and ((resid 57 through 59 and (name N...	B	B	193 - 331	143 - 281
2	4	HIS	HIS	PHE	PHE	(chain 'B' and ((resid 57 through 59 and (name N...	B	B	333 - 408	283 - 358
2	5	ILE	ILE	PHE	PHE	(chain 'B' and ((resid 57 through 59 and (name N...	B	B	417 - 460	367 - 410

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Protein / Protein/peptide , 2 types, 3 molecules ABD

#1: Protein	Tubulin polyglutamylase TTLL6 / Tubulin--tyrosine ligase-like protein 6 Mass: 53373.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Q9E8, Ligases
#2: Protein/peptide	TTLL6 unregistered chain Mass: 954.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Unregistered part of one of the main chains / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 163 molecules

#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO₄
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.29 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 200 mM Ammonium Sulfate, 0.1M Bis Tris pH 5.5, 16% Peg 3350 PH range: 5.2-6.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 2.18→45.93 Å / Num. obs: 105266 / % possible obs: 99.7 % / Redundancy: 2 % / B_iso Wilson estimate: 44.3 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.03045 / R_pim(I) all: 0.02153 / R_rim(I) all: 0.03 / Net I/σ(I): 14.14
Reflection shell	Resolution: 2.18→2.26 Å / Redundancy: 2 % / R_merge(I) obs: 0.2793 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 10288 / CC_1/2: 0.929 / R_pim(I) all: 0.279 / R_rim(I) all: 0.395 / % possible all: 98.59

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YLR

4ylr

Resolution: 2.18→45.93 Å / SU ML: 0.316 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 35.0987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2706	5011	4.87 %
R_work	0.237	97898	-
obs	0.2386	102909	99.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 71.99 Å²

Refinement step

Cycle: LAST / Resolution: 2.18→45.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6176	0	164	141	6481

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	6468
X-RAY DIFFRACTION	f_angle_d	0.5259	8769
X-RAY DIFFRACTION	f_chiral_restr	0.0395	941
X-RAY DIFFRACTION	f_plane_restr	0.003	1110
X-RAY DIFFRACTION	f_dihedral_angle_d	15.3384	2258

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.18-2.21	0.3649	111	0.3698	3124	X-RAY DIFFRACTION	94.59
2.21-2.23	0.364	194	0.3549	3303	X-RAY DIFFRACTION	99.63
2.23-2.26	0.3884	162	0.3567	3229	X-RAY DIFFRACTION	99.82
2.26-2.29	0.3464	178	0.3194	3236	X-RAY DIFFRACTION	99.88
2.29-2.32	0.3983	216	0.3278	3228	X-RAY DIFFRACTION	99.62
2.32-2.35	0.3942	203	0.3361	3273	X-RAY DIFFRACTION	99.51
2.35-2.38	0.4238	129	0.3312	3233	X-RAY DIFFRACTION	99.53
2.38-2.42	0.4275	197	0.3374	3248	X-RAY DIFFRACTION	99.54
2.42-2.46	0.4959	186	0.3409	3315	X-RAY DIFFRACTION	99.89
2.46-2.5	0.3646	155	0.3159	3205	X-RAY DIFFRACTION	99.59
2.5-2.54	0.3256	154	0.299	3300	X-RAY DIFFRACTION	99.57
2.54-2.59	0.4053	137	0.3127	3330	X-RAY DIFFRACTION	99.91
2.59-2.64	0.4237	153	0.3024	3225	X-RAY DIFFRACTION	99.76
2.64-2.69	0.3371	171	0.2868	3290	X-RAY DIFFRACTION	99.6
2.69-2.75	0.3036	130	0.2838	3273	X-RAY DIFFRACTION	99.65
2.75-2.81	0.3503	184	0.2718	3301	X-RAY DIFFRACTION	99.91
2.81-2.88	0.3551	202	0.269	3235	X-RAY DIFFRACTION	99.85
2.88-2.96	0.2929	178	0.2738	3215	X-RAY DIFFRACTION	99.94
2.96-3.05	0.284	171	0.2453	3267	X-RAY DIFFRACTION	100
3.05-3.15	0.3138	179	0.2494	3292	X-RAY DIFFRACTION	100
3.15-3.26	0.3215	177	0.2611	3280	X-RAY DIFFRACTION	100
3.26-3.39	0.268	184	0.2417	3211	X-RAY DIFFRACTION	99.94
3.39-3.54	0.3241	120	0.229	3336	X-RAY DIFFRACTION	100
3.54-3.73	0.253	156	0.2088	3303	X-RAY DIFFRACTION	99.94
3.73-3.96	0.2563	158	0.2093	3289	X-RAY DIFFRACTION	100
3.96-4.27	0.2136	166	0.1946	3228	X-RAY DIFFRACTION	100
4.27-4.7	0.1891	150	0.1773	3310	X-RAY DIFFRACTION	99.94
4.7-5.38	0.2205	158	0.1926	3318	X-RAY DIFFRACTION	100
5.38-6.77	0.2302	180	0.2326	3250	X-RAY DIFFRACTION	100
6.77-45.93	0.186	172	0.2014	3251	X-RAY DIFFRACTION	99.51

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.19036804163	-1.36637554292	1.96993077349	4.80179697429	-1.66008703043	4.54539404474	0.046506967069	0.720015290163	0.383107707237	-1.56694600177	-0.148290475804	-0.182786315011	0.469120035948	0.114744029555	0.0795884168293	0.924990754445	-0.0469522293279	0.0969290606773	0.378088842072	0.0425804645164	0.462139560976	0.324474098046	15.5248747426	35.5542660211
2	2.08634231996	0.270043990317	-0.356042158309	1.55584511472	0.688103097216	0.385628368468	-0.142002373895	-0.445227622499	0.616447086825	0.159813055404	-0.00595133163008	-1.64566448005	-0.177757208696	1.03955594343	0.0906160646482	-0.0400914145566	0.0434361239444	0.384063060063	1.30611100058	0.581984563411	1.43228360463	29.4656729452	6.53717731263	43.643568768
3	3.10313140276	-0.543324997716	-0.668783414627	3.44673711684	0.120670505435	2.7692808597	-0.310584570506	0.0719980781733	-0.404674323778	-0.470261027725	-0.0447960905275	-0.674792599228	0.88165890386	0.66573556303	0.331744422327	0.733235460705	0.0980455687886	0.206801703556	0.524417223274	0.119452907215	0.489428401981	12.384015362	-1.56651547979	42.2988339354
4	2.97766523169	-0.71166603403	0.265991269037	6.02654869926	-1.83031663724	3.23821932342	-0.100861458351	0.165310686402	-0.0175629563627	-0.850596548604	-0.0112050537878	-0.141699999853	0.605946587345	-0.0478260264364	0.0916323630328	0.487068211334	-0.0405810532079	0.0927864167674	0.351569135953	-0.0183619993837	0.259296982083	1.84468699465	6.30110353518	46.6808507724
5	3.40334801439	-2.7467386301	-0.974605449606	4.67870666774	-2.90217713001	5.62681357329	0.365723977234	0.396897846742	0.385653639772	0.767601160561	-0.132693179448	0.432178194799	-1.86093806376	-0.251575227083	-0.247353678644	0.713511544381	-0.0626454104318	-0.0418213523125	0.704919237019	0.103348222394	0.827235019883	-16.233851447	33.6295471452	40.9335187264
6	5.84007265034	1.68035131905	-2.69966276417	8.58209018978	2.9920062204	4.88715510744	0.121515846089	-0.425628926314	0.296060099564	0.266808486767	-0.058185633453	0.139005688379	0.083294934965	-0.144871947069	-0.038966547177	0.367967495205	-0.0117747843622	0.00301080146788	0.359513588093	0.0272663746431	0.279611473938	-5.49595004826	21.7603020556	53.2507492745
7	5.12175850065	1.48147228786	-1.69339269787	4.24010820333	-1.46451081386	3.8397986845	0.220063485579	-0.703121190113	-0.344520092204	1.48805121342	-0.26676216671	-0.11504242931	-0.592933243784	0.0546796948135	0.078295865282	1.01306919581	0.0719377642351	-0.033163676824	0.396260307593	0.0512161359125	0.412629375245	0.846629478196	-20.9925026674	22.1633562773
8	3.61625150255	1.62918357242	1.6479997662	1.71931722869	1.28400319597	1.04133599436	-0.162750853613	1.00578065225	0.679785523048	0.142146811435	0.22950509212	-1.15536441635	-0.181043842876	0.743837481612	-0.0493015888771	0.563731261576	-0.00884568932369	-0.275191713893	1.0780107049	0.317977349267	1.5402268822	32.516450224	-13.3694452501	14.3685358376
9	3.257416074	0.779179437516	0.879665386058	3.68162726638	-0.197975911458	2.64222420458	-0.347876092615	-0.183017506922	0.399292801867	0.781514484647	-0.132340286809	-0.747858045195	-0.857842167325	0.582549272546	0.47799149798	0.957420893413	-0.105224945606	-0.2303478015	0.520908840335	0.131361172177	0.527550101218	13.4614649973	-4.45191459713	15.8409311785
10	2.73551707538	0.560833189433	-0.554243349406	5.73369976203	-1.68103244265	3.24573674755	-0.147866311735	-0.128171570919	0.0218053996246	0.830086317959	0.0447757858273	-0.160033501962	-0.562051152583	-0.143570376119	0.0436004102249	0.4635879115	0.037723670599	-0.0887122054725	0.357774245103	-0.00999959922718	0.265884834141	1.96093329836	-12.2222799611	11.3434597293
11	2.54972976422	-1.60860766917	-0.93637443447	8.58783192074	4.18552204717	3.82175568971	0.0867169189008	-0.0191235402819	-0.455574955591	0.381531470152	-0.330672177172	1.15605129454	1.86033358211	-0.229848978013	0.299863797179	1.09424909634	0.0512625582657	0.0476891749302	0.540346137315	0.0902126935748	0.678474410173	-16.2068840348	-35.5426471153	18.0213105144
12	5.70471358494	-0.506296848671	1.37910256182	8.09788208752	2.34300241327	1.28357072257	0.0674887017749	0.506816299981	-0.351410734279	-0.327691619347	0.00971071962032	0.00882502136971	0.215055141399	-0.102837317945	-0.0830877787998	0.418719161265	0.0596235572201	-0.00524784266871	0.463971409459	-0.00463293287412	0.232795138089	-5.50846325761	-27.4903193403	4.80305170029
13	3.44638143224	0.458399792316	-0.464371414435	5.43150918847	-3.59936857902	2.39052762112	0.172317156013	-0.19786162931	0.347052527552	0.171986706708	0.602410049791	0.0522276035403	-0.278322554613	-0.188054192817	-0.718723573372	1.71115741033	0.0897585620027	0.13187358752	0.674634189545	0.408344531093	1.50168878252	7.64117735988	35.4363901798	30.4612479667

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 57:146)
2	X-RAY DIFFRACTION	2	(chain A and resid 147:175)
3	X-RAY DIFFRACTION	3	(chain A and resid 176:275)
4	X-RAY DIFFRACTION	4	(chain A and resid 276:384)
5	X-RAY DIFFRACTION	5	(chain A and resid 385:421)
6	X-RAY DIFFRACTION	6	(chain A and resid 422:460)
7	X-RAY DIFFRACTION	7	(chain B and resid 57:149)
8	X-RAY DIFFRACTION	8	(chain B and resid 150:169)
9	X-RAY DIFFRACTION	9	(chain B and resid 170:275)
10	X-RAY DIFFRACTION	10	(chain B and resid 276:384)
11	X-RAY DIFFRACTION	11	(chain B and resid 385:420)
12	X-RAY DIFFRACTION	12	(chain B and resid 421:460)
13	X-RAY DIFFRACTION	13	(chain D and resid 7:17)

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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Aug 12, 2020. Covid-19 info

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