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- PDB-8asn: Crystal structure of the apo human TTL in complex with tubulin-st... -

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Basic information

Entry
Database: PDB / ID: 8asn
TitleCrystal structure of the apo human TTL in complex with tubulin-stathmin
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin--tyrosine ligase
KeywordsCELL CYCLE / cytoskeleton / tubulin tyrosine ligase / carbon-nitrogen bonds / amino-acid ligase
Function / homology
Function and homology information


tubulin-tyrosine ligase / Carboxyterminal post-translational modifications of tubulin / regulation of metaphase plate congression / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of axon extension / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule ...tubulin-tyrosine ligase / Carboxyterminal post-translational modifications of tubulin / regulation of metaphase plate congression / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of axon extension / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / positive regulation of mitotic cell cycle / post-translational protein modification / cellular response to interleukin-4 / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family ...: / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain / Tubulin--tyrosine ligase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.571 Å
AuthorsVuillard, L. / Miallau, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the apo human TTL in complex with tubulin-stathmin
Authors: Vuillard, L. / Miallau, L.
History
DepositionAug 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin--tyrosine ligase
G: Tubulin--tyrosine ligase
H: Tubulin--tyrosine ligase
I: Tubulin--tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,28221
Polymers393,2319
Non-polymers4,05112
Water8,251458
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, hTTL is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30620 Å2
ΔGint-149 kcal/mol
Surface area120190 Å2
Unit cell
Length a, b, c (Å)82.553, 199.636, 134.669
Angle α, β, γ (deg.)90, 97.02, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 9 molecules ACBDEFGHI

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16883.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein
Tubulin--tyrosine ligase / TTL


Mass: 43984.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NG68, tubulin-tyrosine ligase

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Non-polymers , 5 types, 470 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#8: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4 % Tacsimate pH 6.0, 12 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98008 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 2.571→133.659 Å / Num. obs: 89154 / % possible obs: 92.6 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.571→2.803 Å / Num. unique obs: 4458 / CC1/2: 0.533

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SA0

1sa0


Resolution: 2.571→133.66 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.422
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 4463 -RANDOM
Rwork0.2428 ---
obs0.2443 89154 65.1 %-
Displacement parametersBiso mean: 67.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.4628 Å20 Å2-1.6488 Å2
2--0.4655 Å20 Å2
3---0.9973 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.571→133.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25448 0 248 458 26154
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00626343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8235721HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9158SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4499HARMONIC5
X-RAY DIFFRACTIONt_it26338HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3361SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact20933SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion17.86
LS refinement shellResolution: 2.571→2.72 Å
RfactorNum. reflection% reflection
Rfree0.3245 82 -
Rwork0.3041 --
obs--8.37 %

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