- PDB-5jpw: Molecular basis for protein recognition specificity of the DYNLT1... -
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Basic information
Entry
Database: PDB / ID: 5jpw
Title
Molecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB
MOTOR PROTEIN / DNYLT1/Tctex-1 / Dynein Intermediate Chain / Dynein motor / Dynein-mediated transport
Function / homology
Function and homology information
intracellular transport of viral protein in host cell / secretory vesicle / transport along microtubule / dynein light chain binding / dynein heavy chain binding / dynein complex / regulation of G protein-coupled receptor signaling pathway / COPI-independent Golgi-to-ER retrograde traffic / microtubule-dependent intracellular transport of viral material towards nucleus / cytoplasmic dynein complex ...intracellular transport of viral protein in host cell / secretory vesicle / transport along microtubule / dynein light chain binding / dynein heavy chain binding / dynein complex / regulation of G protein-coupled receptor signaling pathway / COPI-independent Golgi-to-ER retrograde traffic / microtubule-dependent intracellular transport of viral material towards nucleus / cytoplasmic dynein complex / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / establishment of mitotic spindle orientation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / RHO GTPases Activate Formins / negative regulation of neurogenesis / Aggrephagy / spindle / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / host cell / nervous system development / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / microtubule / symbiont entry into host cell / cell division / centrosome / Neutrophil degranulation / Golgi apparatus / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function
Mass: 15431.400 Da / Num. of mol.: 2 / Fragment: UNP residues 1-113,UNP residues 134-154 Source method: isolated from a genetically manipulated source Details: Residues G1 to S2 correspond to the expression tag. Residues M3 to I115 correspond to the whole sequence of dynein light chain Tctex-type 1 (H. sapiens, UNIPROT entry P63172). Residues G116 ...Details: Residues G1 to S2 correspond to the expression tag. Residues M3 to I115 correspond to the whole sequence of dynein light chain Tctex-type 1 (H. sapiens, UNIPROT entry P63172). Residues G116 to S122 correspond to a designed linker sequence. Residues G123 to V143 correspond to residues G134 to V154 of Cytoplasmic dynein 1 intermediate chain 2 (H. sapiens, UNIPROT entry Q13409) Source: (gene. exp.) Homo sapiens (human) Gene: DYNLT1, TCTEL1, TCTEX-1, TCTEX1, DYNC1I2, DNCI2, DNCIC2 Production host: Escherichia coli (E. coli) / References: UniProt: P63172, UniProt: Q13409
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
1
2D 1H-1H NOESY
1
11
1
isotropic
1
2D 1H-1H TOCSY
1
3
1
isotropic
1
2D 1H-13C HSQC
1
2
2
isotropic
1
2D 1H-15N HSQC
1
4
3
isotropic
1
3DCBCA(CO)NH
1
5
3
isotropic
1
3D HN(CA)CB
1
6
3
isotropic
1
3D HNCA
1
7
3
isotropic
1
3DHN(CO)CA
1
8
3
isotropic
1
3D (H)CCH-TOCSY
1
9
3
isotropic
1
3D 1H-13C NOESY aliphatic
1
10
3
isotropic
1
3D 1H-13C NOESY aromatic
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Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
1
100 uM DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O
Non-labelled_sample
90% H2O/10% D2O
solution
2
100 uM [U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O
15N_labelled_sample
90% H2O/10% D2O
solution
3
100 uM [U-99% 13C; U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O
15N_13C_labelled
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
100uM
DYNLT1/Tctex1-DIC chimera
naturalabundance
1
100mM
potassiumphosphate
naturalabundance
1
1mM
DTT
naturalabundance
1
50uM
DSS
naturalabundance
1
100uM
DYNLT1/Tctex1-DIC chimera
[U-99% 15N]
2
100mM
potassiumphosphate
naturalabundance
2
1mM
DTT
naturalabundance
2
50uM
DSS
naturalabundance
2
100uM
DYNLT1/Tctex1-DIC chimera
[U-99% 13C; U-99% 15N]
3
100mM
potassiumphosphate
naturalabundance
3
1mM
DTT
naturalabundance
3
50uM
DSS
naturalabundance
3
Sample conditions
Ionic strength units: Not defined / Label: Standard_conditions / pH: 7 / Pressure: 1 atm / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: With triple resonance z-gradient cryoprobe
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