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- PDB-5yi4: Solution Structure of the DISC1/Ndel1 complex -

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Basic information

Entry
Database: PDB / ID: 5yi4
TitleSolution Structure of the DISC1/Ndel1 complex
ComponentsDisrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1
KeywordsPROTEIN BINDING / DISC1 / Ndel1 / coiled coil / psychiatric disorder
Function / homology
Function and homology information


neurofilament cytoskeleton / pyramidal neuron migration to cerebral cortex / cerebral cortex radially oriented cell migration / establishment of chromosome localization / central nervous system neuron axonogenesis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / radial glia-guided pyramidal neuron migration / mitochondrial calcium ion homeostasis / central region of growth cone / cell proliferation in forebrain ...neurofilament cytoskeleton / pyramidal neuron migration to cerebral cortex / cerebral cortex radially oriented cell migration / establishment of chromosome localization / central nervous system neuron axonogenesis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / radial glia-guided pyramidal neuron migration / mitochondrial calcium ion homeostasis / central region of growth cone / cell proliferation in forebrain / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / oligopeptidase activity / regulation of dendritic spine development / RHO GTPases Activate Formins / nuclear membrane disassembly / Separation of Sister Chromatids / vesicle transport along microtubule / neurofilament cytoskeleton organization / lysosome localization / dynein complex / axon hillock / microtubule nucleation / regulation of synapse maturation / non-motile cilium assembly / positive regulation of ubiquitin-dependent protein catabolic process / retrograde axonal transport / mitotic centrosome separation / positive regulation of ruffle assembly / protein localization to centrosome / microtubule organizing center / microtubule associated complex / intermediate filament cytoskeleton / inner cell mass cell proliferation / centrosome localization / positive regulation of cell-matrix adhesion / neuron projection extension / regulation of postsynapse organization / kinesin complex / ciliary base / positive regulation of neuroblast proliferation / regulation of intracellular protein transport / positive regulation of axon regeneration / regulation of neuron projection development / cell leading edge / beta-tubulin binding / establishment of mitotic spindle orientation / detection of temperature stimulus involved in sensory perception of pain / kinesin binding / positive regulation of Wnt signaling pathway / cilium assembly / alpha-tubulin binding / TOR signaling / positive regulation of axon extension / canonical Wnt signaling pathway / response to electrical stimulus / GABA-ergic synapse / axon cytoplasm / regulation of synaptic transmission, glutamatergic / ciliary basal body / negative regulation of protein binding / chromosome segregation / neuron migration / kinetochore / positive regulation of neuron projection development / microtubule cytoskeleton organization / spindle / neuron cellular homeostasis / neuron projection development / protein localization / cell migration / synaptic vesicle / insulin receptor signaling pathway / nuclear envelope / nervous system development / cell body / ubiquitin-dependent protein catabolic process / microtubule binding / microtubule / molecular adaptor activity / postsynaptic density / axon / centrosome / glutamatergic synapse / protein-containing complex binding / perinuclear region of cytoplasm / mitochondrion / identical protein binding / cytosol
Similarity search - Function
NUDE domain / Disrupted in schizophrenia 1 / NUDE family / NUDE protein, C-terminal conserved region
Similarity search - Domain/homology
Disrupted in schizophrenia 1 homolog / Nuclear distribution protein nudE-like 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsYe, F. / Yu, C. / Yu, C. / Zhang, M.
Funding support Hong Kong, China, 5items
OrganizationGrant numberCountry
RGC664113 Hong Kong
RGC16103614 Hong Kong
RGCAoE-M09-12 Hong Kong
RGCT13-607/12R Hong Kong
Minister of Science and Technology of China2014CB910204 China
CitationJournal: Neuron / Year: 2017
Title: DISC1 Regulates Neurogenesis via Modulating Kinetochore Attachment of Ndel1/Nde1 during Mitosis.
Authors: Ye, F. / Kang, E. / Yu, C. / Qian, X. / Jacob, F. / Yu, C. / Mao, M. / Poon, R.Y.C. / Kim, J. / Song, H. / Ming, G.L. / Zhang, M.
History
DepositionOct 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_nmr_software.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: Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1


Theoretical massNumber of molelcules
Total (without water)15,4551
Polymers15,4551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11450 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1 / Protein mNudE-like / mNudE-L


Mass: 15455.417 Da / Num. of mol.: 1 / Fragment: UNP residues 765-852,UNP residues 238-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Disc1, Ndel1, Nudel
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q811T9, UniProt: Q9ERR1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114anisotropic22D 1H-1H NOESY
121isotropic23D 1H-13C NOESY
132isotropic23D 1H-15N NOESY
143isotropic23D CBCA(CO)NH
153isotropic23D HN(CA)CB

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] DISC1_Ndel1, 100% D2O13C and 15N sample100% D2O
solution30.8 mM [U-99% 13C; U-99% 15N] DISC1_Ndel1, 90% H2O/10% D2O13C and 15N sample in H2O90% H2O/10% D2O
solution20.8 mM [U-99% 15N] DISC1_Ndel1, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solid40.8 mM no labelling DISC1_Ndel1, 100% D2Ono labelling100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDISC1_Ndel1[U-99% 13C; U-99% 15N]1
0.8 mMDISC1_Ndel1[U-99% 13C; U-99% 15N]3
0.8 mMDISC1_Ndel1[U-99% 15N]2
0.8 mMDISC1_Ndel1no labelling4
Sample conditionsIonic strength: 50 NaCl mM / Ionic strength err: 0.2 / Label: conditions_1 / pH: 6.5 / Pressure: 1 Pa / Pressure err: 0.01 / Temperature: 303 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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