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- PDB-7c1m: Complex structure of tyrosinated alpha-tubulin carboxy-terminal p... -

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Basic information

Entry
Database: PDB / ID: 7c1m
TitleComplex structure of tyrosinated alpha-tubulin carboxy-terminal peptide and A1aY1 binder
Components
  • Carboxy-terminal peptide from tyrosinated alpha-tubulin
  • Nanobody binder from SSO7d library
KeywordsPROTEIN BINDING / Tyrosinated / Microtubule / Binder / SSO7d / yeast display
Function / homology
Function and homology information


pyramidal neuron differentiation / glial cell differentiation / Post-chaperonin tubulin folding pathway / cytoskeleton-dependent intracellular transport / Cargo trafficking to the periciliary membrane / dentate gyrus development / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / axonemal microtubule / organelle transport along microtubule ...pyramidal neuron differentiation / glial cell differentiation / Post-chaperonin tubulin folding pathway / cytoskeleton-dependent intracellular transport / Cargo trafficking to the periciliary membrane / dentate gyrus development / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / axonemal microtubule / organelle transport along microtubule / forebrain morphogenesis / cerebellar cortex morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / microtubule plus-end / neuron projection arborization / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / smoothened signaling pathway / homeostasis of number of cells within a tissue / motor behavior / Kinesins / Prefoldin mediated transfer of substrate to CCT/TriC / response to L-glutamate / Assembly and cell surface presentation of NMDA receptors / COPI-independent Golgi-to-ER retrograde traffic / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / startle response / 'de novo' protein folding / flagellated sperm motility / regulation of synapse organization / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / response to tumor necrosis factor / response to mechanical stimulus / neuron apoptotic process / adult locomotory behavior / sperm flagellum / RHO GTPases activate IQGAPs / Hedgehog 'off' state / COPI-mediated anterograde transport / microtubule-based process / condensed chromosome / Activation of AMPK downstream of NMDARs / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / visual learning / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / intracellular protein transport / neuron migration / memory / cerebral cortex development / RHO GTPases Activate Formins / synapse organization / PKR-mediated signaling / recycling endosome / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / microtubule cytoskeleton / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / neuron differentiation / cilium / protein-folding chaperone binding / microtubule / microtubule binding / cell division / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein stabilization / protein heterodimerization activity / GTPase activity / GTP binding / protein-containing complex binding / structural molecule activity / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Alpha 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 ...Alpha 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
Similarity search - Domain/homology
Tubulin alpha-1A chain
Similarity search - Component
Biological speciesSaccharolobus solfataricus 98/2 (archaea)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKesarwani, S. / Reddy, P.P. / Sirajuddin, M. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR5081/INF/156/2012 India
CitationJournal: J.Cell Biol. / Year: 2020
Title: Genetically encoded live-cell sensor for tyrosinated microtubules.
Authors: Kesarwani, S. / Lama, P. / Chandra, A. / Reddy, P.P. / Jijumon, A.S. / Bodakuntla, S. / Rao, B.M. / Janke, C. / Das, R. / Sirajuddin, M.
History
DepositionMay 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody binder from SSO7d library
B: Carboxy-terminal peptide from tyrosinated alpha-tubulin


Theoretical massNumber of molelcules
Total (without water)8,8422
Polymers8,8422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area5270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Nanobody binder from SSO7d library


Mass: 7486.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus 98/2 (archaea)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide Carboxy-terminal peptide from tyrosinated alpha-tubulin


Mass: 1355.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71U36*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HN(CA)CB
1101isotropic13D CBCA(CO)NH
191isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic22D Filtered NOESY
1111isotropic22D Filtered TOCSY
1121isotropic23D 13C-filtered, 13C-edited NOESY

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Sample preparation

DetailsType: solution
Contents: 50 mM unlabeled sodium phosphate, 200 mM unlabeled sodium chloride, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphateunlabeled1
200 mMsodium chlorideunlabeled1
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
HADDOCKBonvinstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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