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- PDB-2e4h: Solution structure of cytoskeletal protein in complex with tubuli... -

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Basic information

Entry
Database: PDB / ID: 2e4h
TitleSolution structure of cytoskeletal protein in complex with tubulin tail
Components
  • Restin
  • Tubulin alpha-ubiquitous chain
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / CAP-Gly / complex structure / tubulin / solution structure / CLIP
Function / homology
Function and homology information


Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic ...Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / microtubule bundle formation / Kinesins / Assembly and cell surface presentation of NMDA receptors / intermediate filament / COPI-dependent Golgi-to-ER retrograde traffic / Recycling pathway of L1 / RHOH GTPase cycle / RHO GTPases activate IQGAPs / Hedgehog 'off' state / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / ruffle / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / cellular response to interleukin-4 / tubulin binding / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / cytoplasmic vesicle membrane / structural constituent of cytoskeleton / microtubule cytoskeleton organization / kinetochore / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / cell cortex / microtubule binding / microtubule / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / structural molecule activity / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Alpha tubulin ...CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CAP-Gly domain-containing linker protein 1 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMishima, M. / Hakoshima, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for tubulin recognition by cytoplasmic linker protein 170 and its autoinhibition
Authors: Mishima, M. / Maesaki, R. / Kasa, M. / Watanabe, T. / Fukata, M. / Kaibuchi, K. / Hakoshima, T.
History
DepositionDec 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Restin
B: Tubulin alpha-ubiquitous chain


Theoretical massNumber of molelcules
Total (without water)14,5562
Polymers14,5562
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Restin / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament-associated ...Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament-associated protein / Cytoplasmic linker protein 1


Mass: 10540.216 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain 2, residues 203-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP-170 / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30622
#2: Protein/peptide Tubulin alpha-ubiquitous chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Alpha-tubulin 3


Mass: 4016.046 Da / Num. of mol.: 1 / Fragment: C-tail, residues 416-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: a3-tubulin / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Star) / References: UniProt: P68363

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
1443D 15N-separated NOESY
NMR detailsText: Standard heteronuclear NMR technique and NH RDCs

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9mM U-15N,13C CLIP: Nonlabel tubulin; 30mM BisTris buffer K; 1mM DTT; 100% D2O100% D2O
20.9mM U-15N CLIP: Nonlabel tubulin; 30mM BisTris buffer K; 1mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
30.9mM U-15N,13C tubulin: Nonlabel CLIP; 30mM BisTris buffer K; 1mM DTT; 100% D2O100% D2O
40.9mM U-15N tubulin: Nonlabel CLIP; 30mM BisTris buffer K; 1mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionspH: 6.9 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4F. Delaglioprocessing
Sparky3.1.10T. D. Goddard and D. G. Knellerdata analysis
CYANA2.1P. Guntertstructure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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