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- PDB-9hq4: TTLL11 bound to microtubule -

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Basic information

Entry
Database: PDB / ID: 9hq4
TitleTTLL11 bound to microtubule
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin polyglutamylase TTLL11
KeywordsLIGASE / TTLL11 / polyglutamylase / tubulin / microtubule
Function / homology
Function and homology information


tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / microtubule severing / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane ...tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / microtubule severing / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / haloalkane dehalogenase / haloalkane dehalogenase activity / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / Kinesins / GTPase activating protein binding / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / nuclear envelope lumen / regulation of synapse organization / Recycling pathway of L1 / MHC class I protein binding / RHOH GTPase cycle / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / intercellular bridge / spindle assembly / cytoplasmic microtubule / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / cellular response to interleukin-4 / tubulin binding / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / PKR-mediated signaling / protein modification process / structural constituent of cytoskeleton / response to toxic substance / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / cell body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Potential therapeutics for SARS / microtubule / cytoskeleton / cilium / ciliary basal body / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...Haloalkane dehalogenase, subfamily 2 / : / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / TAXOL / Tubulin beta chain / Haloalkane dehalogenase / Tubulin alpha-1B chain / Tubulin polyglutamylase TTLL11
Similarity search - Component
Biological speciesPseudomonas pavonaceae (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBarinka, C. / Campbell, J. / Desfosses, A. / Gutsche, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation23-07149S Czech Republic
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic insights into TTLL11 polyglutamylase-mediated primary tubulin chain elongation.
Authors: Jana Campbell / Miroslava Vosahlikova / Samar Ismail / Margareta Volnikova / Lucia Motlova / Julia Kudlacova / Kseniya Ustinova / Ivan Snajdr / Zora Novakova / Miroslav Basta / Irina Gutsche ...Authors: Jana Campbell / Miroslava Vosahlikova / Samar Ismail / Margareta Volnikova / Lucia Motlova / Julia Kudlacova / Kseniya Ustinova / Ivan Snajdr / Zora Novakova / Miroslav Basta / Irina Gutsche / Marie-Jo Moutin / Ambroise Desfosses / Cyril Barinka /
Abstract: Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification ...Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification targeting unstructured tubulin C-terminal tails-plays a pivotal role in defining the tubulin code. Here, we describe a mechanism by which tubulin tyrosine ligase-like 11 (TTLL11) expands and diversifies the code. Cryo-electron microscopy revealed a unique bipartite MT recognition strategy wherein TTLL11 binding and catalytic domains engage adjacent MT protofilaments. Biochemical and cellular assays identified previously uncharacterized polyglutamylation patterns, showing that TTLL11 directly extends the primary polypeptide chains of α- and β-tubulin in vitro, challenging the prevailing paradigms emphasizing lateral branching. Moreover, cell-based and in vivo data suggest a cross-talk between polyglutamylation and the detyrosination/tyrosination cycle likely linked to the TTLL11-mediated elongation of the primary α-tubulin chain. These findings unveil an unrecognized layer of complexity within the tubulin code and offer mechanistic insights into the molecular basis of functional specialization of MT cytoskeleton.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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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 chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Tubulin polyglutamylase TTLL11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,14415
Polymers311,2545
Non-polymers3,89010
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 5 molecules ACBDE

#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
Details: Native tubulin isolated from HEK 293T cells, unaligned regions are intrinsicly disordered
Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Plasmid details: suspension cell culture / References: UniProt: P68363
#2: Protein Tubulin beta chain / Tubulin beta-5 chain


Mass: 49717.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The C-terminal part of tubulin is intrinsicaly disordered thus not visible in the structure.
Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Plasmid details: suspension cell culture / References: UniProt: P07437
#3: Protein Tubulin polyglutamylase TTLL11 / Tubulin--tyrosine ligase-like protein 11


Mass: 111410.188 Da / Num. of mol.: 1 / Mutation: E441G
Source method: isolated from a genetically manipulated source
Details: The original protein contains N-terminal Halo tag on a flexible linker so it is not visible in the map or included in the model. TTLL11 containes several instriscally disordered regions that ...Details: The original protein contains N-terminal Halo tag on a flexible linker so it is not visible in the map or included in the model. TTLL11 containes several instriscally disordered regions that are left out from the model.
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria), (gene. exp.) Homo sapiens (human)
Gene: TTLL11, C9orf20 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P0A3G4, UniProt: Q8NHH1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 3 types, 10 molecules

#4: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of TTLL11 and two tubulin dimers / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293T
Buffer solutionpH: 7
Details: 40 mM Tris-HCl, pH 7.0, 1 mM TCEP, 1 mM MgCl2, 5 % glycerol
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239587 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingAccession code: AF-Q8NHH1-F1-v4 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418271
ELECTRON MICROSCOPYf_angle_d0.60324812
ELECTRON MICROSCOPYf_dihedral_angle_d8.6082825
ELECTRON MICROSCOPYf_chiral_restr0.0442727
ELECTRON MICROSCOPYf_plane_restr0.0053197

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