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- PDB-5jpw: Molecular basis for protein recognition specificity of the DYNLT1... -

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Basic information

Entry
Database: PDB / ID: 5jpw
TitleMolecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB
ComponentsDynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2
KeywordsMOTOR 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
Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / : / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / : / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Dynein light chain Tctex-type 1 / Cytoplasmic dynein 1 intermediate chain 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsRodriguez-Crespo, I. / Merino-Gracia, J. / Bruix, M. / Zamora-Carreras, H.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2012-37934 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2014-52633-P Spain
Comunidad de MadridS2010/BMD-2305 Spain
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis for the Protein Recognition Specificity of the Dynein Light Chain DYNLT1/Tctex1: CHARACTERIZATION OF THE INTERACTION WITH ACTIVIN RECEPTOR IIB.
Authors: Merino-Gracia, J. / Zamora-Carreras, H. / Bruix, M. / Rodriguez-Crespo, I.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jul 3, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2
B: Dynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2


Theoretical massNumber of molelcules
Total (without water)30,8632
Polymers30,8632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2230 Å2
ΔGint-19 kcal/mol
Surface area19590 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Dynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2 / Protein CW-1 / T-complex testis-specific protein 1 homolog / Cytoplasmic dynein intermediate chain ...Protein CW-1 / T-complex testis-specific protein 1 homolog / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


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

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
1111isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
122isotropic12D 1H-15N HSQC
143isotropic13D CBCA(CO)NH
153isotropic13D HN(CA)CB
163isotropic13D HNCA
173isotropic13D HN(CO)CA
183isotropic13D (H)CCH-TOCSY
193isotropic13D 1H-13C NOESY aliphatic
1103isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1100 uM DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2ONon-labelled_sample90% H2O/10% D2O
solution2100 uM [U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O15N_labelled _sample90% H2O/10% D2O
solution3100 uM [U-99% 13C; U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O15N_13C_labelled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMDYNLT1/Tctex1-DIC chimeranatural abundance1
100 mMpotassium phosphatenatural abundance1
1 mMDTTnatural abundance1
50 uMDSSnatural abundance1
100 uMDYNLT1/Tctex1-DIC chimera[U-99% 15N]2
100 mMpotassium phosphatenatural abundance2
1 mMDTTnatural abundance2
50 uMDSSnatural abundance2
100 uMDYNLT1/Tctex1-DIC chimera[U-99% 13C; U-99% 15N]3
100 mMpotassium phosphatenatural abundance3
1 mMDTTnatural abundance3
50 uMDSSnatural abundance3
Sample conditionsIonic strength units: Not defined / Label: Standard_conditions / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: With triple resonance z-gradient cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
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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