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- PDB-6vzu: TTLL6 bound to alpha-elongation analog -

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Basic information

Entry
Database: PDB / ID: 6vzu
TitleTTLL6 bound to alpha-elongation analog
Components
  • (TTLL6 unregistered ...) x 2
  • Tubulin polyglutamylase TTLL6
KeywordsLIGASE / TTLL6 / glutamylase / amino-acid ligase / phosphinic acid inhibitors
Function / homology
Function and homology information


positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / 9+0 non-motile cilium / microtubule severing / regulation of cilium beat frequency involved in ciliary motility ...positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / 9+0 non-motile cilium / microtubule severing / regulation of cilium beat frequency involved in ciliary motility / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / microtubule bundle formation / tubulin binding / microtubule / ciliary basal body / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-RZP / Chem-RZV / Tubulin polyglutamylase TTLL6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMahalingan, K.K. / Keenen, E.K. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.B. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)ZIA NS003163 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)ZIA NS003122 United States
CitationJournal: 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
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin polyglutamylase TTLL6
B: Tubulin polyglutamylase TTLL6
C: Tubulin polyglutamylase TTLL6
D: Tubulin polyglutamylase TTLL6
M: TTLL6 unregistered chain
N: TTLL6 unregistered chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,44641
Polymers215,9136
Non-polymers5,53435
Water18,5191028
1
A: Tubulin polyglutamylase TTLL6
M: TTLL6 unregistered chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81111
Polymers54,4982
Non-polymers1,3139
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6519
Polymers53,3731
Non-polymers1,2778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7287
Polymers53,3731
Non-polymers1,3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tubulin polyglutamylase TTLL6
N: TTLL6 unregistered chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25714
Polymers54,6682
Non-polymers1,58912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.263, 110.631, 173.370
Angle α, β, γ (deg.)90.00, 90.24, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN 'A' AND (RESID 58 THROUGH 81 OR RESID 83...
211(CHAIN 'B' AND (RESID 58 THROUGH 81 OR RESID 83...
311(CHAIN 'C' AND (RESID 58 THROUGH 81 OR RESID 83...
411(CHAIN 'D' AND (RESID 58 THROUGH 81 OR RESID 83...
112CHAIN 'M'
212(CHAIN 'N' AND RESID 9 THROUGH 21)

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tubulin polyglutamylase TTLL6 / Tubulin--tyrosine ligase-like protein 6


Mass: 53373.387 Da / Num. of mol.: 4
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

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TTLL6 unregistered ... , 2 types, 2 molecules MN

#2: Protein/peptide TTLL6 unregistered chain


Mass: 1124.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Unregistered part of one of the chains A,B,C,D / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli)
#3: Protein/peptide TTLL6 unregistered chain


Mass: 1294.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Unregistered part of one of the chains A,B,C,D / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 1063 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical
ChemComp-RZP / (2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 433.242 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C12H21NO12P2
#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-RZV / (2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-oxidanyl-phosphoryl]methyl]pentanedioic acid


Mass: 353.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H20NO9P
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1028 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Sodium Citrate, pH 6.2, 200 mM MgCl2, 8-12% Peg 20000
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→46.63 Å / Num. obs: 193528 / % possible obs: 97.88 % / Redundancy: 6.4 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Rrim(I) all: 0.116 / Χ2: 1.045 / Net I/σ(I): 16.23
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 18563 / CC1/2: 0.845 / CC star: 0.957 / Rpim(I) all: 0.239 / Rrim(I) all: 0.577 / Χ2: 0.957 / % possible all: 94.57

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLR

4ylr


Resolution: 1.98→46.63 Å / SU ML: 0.194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.527
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.193 9690 5.01 %
Rwork0.174 --
obs0.175 193527 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.87 Å2
Refinement stepCycle: LAST / Resolution: 1.98→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12882 0 345 1028 14255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813797
X-RAY DIFFRACTIONf_angle_d0.94618731
X-RAY DIFFRACTIONf_dihedral_angle_d16.0298292
X-RAY DIFFRACTIONf_chiral_restr0.0562014
X-RAY DIFFRACTIONf_plane_restr0.0052383
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13CX-RAY DIFFRACTIONPOSITIONAL
14DX-RAY DIFFRACTIONPOSITIONAL
21MX-RAY DIFFRACTIONPOSITIONAL
22NX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.27742830.24025524X-RAY DIFFRACTION89
2-2.020.23993460.20845855X-RAY DIFFRACTION94
2.02-2.050.22632960.1965958X-RAY DIFFRACTION95
2.05-2.070.24033200.18965929X-RAY DIFFRACTION95
2.07-2.10.21013370.19095981X-RAY DIFFRACTION96
2.1-2.130.22923070.18795991X-RAY DIFFRACTION96
2.13-2.160.21763520.18485987X-RAY DIFFRACTION96
2.16-2.190.2063070.18026077X-RAY DIFFRACTION97
2.19-2.230.20123050.17916064X-RAY DIFFRACTION96
2.23-2.260.22362950.18276016X-RAY DIFFRACTION97
2.26-2.30.20633180.17626107X-RAY DIFFRACTION97
2.3-2.340.20353330.17756088X-RAY DIFFRACTION97
2.34-2.390.21223240.17396100X-RAY DIFFRACTION98
2.39-2.440.22213210.18556165X-RAY DIFFRACTION98
2.44-2.490.22893270.18376173X-RAY DIFFRACTION99
2.49-2.550.22053140.18366175X-RAY DIFFRACTION99
2.55-2.610.2252860.18836242X-RAY DIFFRACTION99
2.61-2.680.21543020.18476243X-RAY DIFFRACTION99
2.68-2.760.23923210.18586209X-RAY DIFFRACTION99
2.76-2.850.21253190.18226236X-RAY DIFFRACTION99
2.85-2.950.19663280.17836252X-RAY DIFFRACTION100
2.95-3.070.20673840.17116213X-RAY DIFFRACTION100
3.07-3.210.18043470.17996234X-RAY DIFFRACTION100
3.21-3.380.18993040.1766324X-RAY DIFFRACTION100
3.38-3.590.21183050.16996303X-RAY DIFFRACTION99
3.59-3.870.16963660.15316185X-RAY DIFFRACTION100
3.87-4.260.15223100.15116270X-RAY DIFFRACTION99
4.26-4.870.15513060.14426263X-RAY DIFFRACTION99
4.87-6.140.1873870.18066290X-RAY DIFFRACTION100
6.14-46.630.17693400.1926383X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°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)
14.93550.7037-0.34836.1982-0.40178.59170.1489-1.03190.07390.8708-0.05250.5556-0.2747-0.7048-0.07580.318-0.00010.07230.45860.05220.2851-1.4788-28.201921.4764
21.53570.71030.57735.0942-0.99632.880.0796-0.19280.09450.4063-0.1386-0.779-0.18530.42110.0810.2344-0.0223-0.06370.3095-0.03240.372529.5152-12.538316.5963
32.60530.2113-0.68262.3883-1.02744.40510.0670.01740.02760.0774-0.0301-0.1409-0.15170.0325-0.02970.1508-0.0055-0.04840.178-0.0040.250821.3661-25.96585.8065
45.56921.9036-0.82373.9308-0.82972.18360.1337-0.4289-0.1340.3452-0.06030.14120.0088-0.114-0.07120.20680.019-0.03460.20790.00790.234211.7056-30.673914.6948
51.99251.98422.01538.8708-8.83579.0409-0.4286-3.5357-0.550.71931.65030.5312-0.2028-2.8213-1.24130.76680.2444-0.03331.08790.06170.63117.1066-44.671546.5981
62.0930.1951.4292.3487-2.01276.24760.086-0.6868-0.50160.6792-0.1106-0.44670.36730.04-0.02140.5340.0272-0.13110.42850.11730.488718.5288-42.642326.3167
74.4807-0.4288-0.09876.99650.41977.59420.25170.67080.046-1.0847-0.2103-0.83450.00340.7003-0.03050.34710.06170.09470.3936-0.03860.275439.9069-54.36669.3078
80.8468-1.66640.5244.93820.45581.2580.36970.3890.0508-0.972-0.20540.51770.1857-0.0839-0.12590.48460.053-0.16310.3994-0.02780.297413.3282-45.629964.2518
91.2469-0.24680.19382.9329-0.79761.9258-0.0156-0.05270.1382-0.00890.09320.3652-0.2216-0.137-0.06980.16120.0007-0.04230.2438-0.04520.281313.3126-42.026581.0658
102.00219.4737.9722.00125.54732.00440.7834-0.9166-1.01641.8295-0.0628-0.99460.1809-0.1405-0.69940.5395-0.0185-0.12610.62610.00850.388423.0935-51.98997.2485
111.935-0.0798-0.64652.2136-0.73952.65820.02320.3469-0.2255-0.6195-0.05260.09420.41820.01460.05880.36150.0382-0.07190.2418-0.09720.258221.8463-58.292571.1822
121.20040.38541.86550.42991.45066.11120.310.7297-0.8818-0.8562-0.09560.48760.57620.3143-0.2260.83450.0508-0.17950.5246-0.23680.630618.5325-68.614460.7474
133.9798-0.7195-1.1084.2342-0.24188.15750.1436-0.7554-0.11731.199-0.1214-0.75960.09010.6896-0.01850.5019-0.0679-0.12590.4007-0.03170.288839.847317.91318.5721
141.96450.5494-0.20873.3289-0.18022.37420.1931-0.4437-0.02830.7882-0.06880.2715-0.1731-0.1523-0.09920.5709-0.05350.13840.3573-0.05470.230617.563414.44724.0839
152.72610.6124-0.95454.9496-1.9414.38230.0658-0.0954-0.13740.36190.13880.92250.116-0.5916-0.17790.2738-0.02110.09420.2763-0.02120.41016.603-1.468813.1811
163.26171.27912.20756.26373.79876.16940.09660.1557-0.15220.001-0.05380.16950.2488-0.0181-0.03740.17340.0040.05360.18720.01030.186517.290711.74381.6921
171.6380.14690.2642.7801-1.05431.72340.0999-0.32170.2440.7909-0.08930.1084-0.46690.00420.0280.4362-0.04730.06590.252-0.10730.226622.146722.54115.4301
182.71360.2768-1.24811.54181.43114.85330.4145-0.82161.11741.0584-0.12470.6244-0.71270.2054-0.24840.7537-0.02740.15790.44-0.18480.597318.659832.409821.9049
194.3882-0.61830.47616.4497-0.49248.66620.12451.0146-0.0295-0.8782-0.05740.5430.2173-0.6827-0.05020.3010.0058-0.05910.47840.04970.2925-1.8627-7.489865.2385
201.2919-0.8738-0.64.4555-0.562.31170.06490.1663-0.0565-0.4327-0.1063-0.78110.14980.41980.06410.22030.01750.0630.3335-0.03120.394128.9533-23.21369.6536
212.0193-0.1306-0.14022.4849-0.70493.82350.06090.05440.0164-0.1272-0.008-0.11860.0516-0.1239-0.05330.14310.00040.0330.23340.01170.307920.5276-9.560279.4096
224.1817-1.19251.08912.8452-0.89562.66270.05330.17390.0616-0.11230.02890.1748-0.0796-0.2203-0.08710.1653-0.01270.03710.19250.00480.241511.2798-5.193272.8612
237.53427.5297-9.27318.1279-8.69952.0020.00134.10390.2957-1.78031.27680.33160.4274-3.2616-1.27221.0237-0.17630.05511.41030.09250.5128.70559.368838.2316
242.87640.0237-2.29741.8609-2.09737.81460.10150.60590.4154-0.6494-0.094-0.4552-0.47750.0311-0.05550.5388-0.06020.10240.36920.10810.47918.66636.61760.9745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 57:115)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 116:204)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 205:329)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 330:398)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 399:417)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 418:461)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 58:100)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 101:163)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 164:274)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 275:280)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 281:413)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 414:461)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 58:105)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 106:143)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 144:205)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 206:279)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 280:425)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 426:461)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 57:114)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 115:203)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 204:336)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 337:401)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 402:417)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 418:461)

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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