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Yorodumi- PDB-2bkd: Structure of the N-terminal domain of Fragile X Mental Retardatio... -
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-Basic information
Entry | Database: PDB / ID: 2bkd | ||||||||||||
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Title | Structure of the N-terminal domain of Fragile X Mental Retardation Protein | ||||||||||||
Components | Fragile X messenger ribonucleoprotein 1 | ||||||||||||
Keywords | NUCLEAR PROTEIN / FMRP / PROTEIN-PROTEIN INTERACTION / MRNA TRANSPORT | ||||||||||||
Function / homology | Function and homology information positive regulation of intracellular transport of viral material / negative regulation of mRNA catabolic process / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule ...positive regulation of intracellular transport of viral material / negative regulation of mRNA catabolic process / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule / non-membrane-bounded organelle assembly / negative regulation of voltage-gated calcium channel activity / regulation of dendritic spine development / messenger ribonucleoprotein complex / dendritic filopodium / RNA strand annealing activity / chromocenter / regulation of neurotransmitter secretion / filopodium tip / : / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / positive regulation of proteasomal protein catabolic process / N6-methyladenosine-containing RNA reader activity / siRNA binding / : / poly(A) binding / RNA stem-loop binding / regulatory ncRNA-mediated gene silencing / glutamate receptor signaling pathway / sequence-specific mRNA binding / miRNA binding / poly(U) RNA binding / positive regulation of dendritic spine development / positive regulation of filopodium assembly / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / dynein complex binding / dendritic spine neck / glial cell projection / positive regulation of receptor internalization / translation regulator activity / chromosome, centromeric region / mRNA transport / Cajal body / negative regulation of cytoplasmic translation / mRNA export from nucleus / signaling adaptor activity / axon terminus / translation initiation factor binding / stress granule assembly / negative regulation of translational initiation / translation repressor activity / methylated histone binding / regulation of mRNA stability / molecular condensate scaffold activity / RNA splicing / positive regulation of translation / mRNA 3'-UTR binding / cell projection / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / mRNA processing / cellular response to virus / cytoplasmic stress granule / ribosome binding / presynapse / presynaptic membrane / chromosome / nervous system development / growth cone / G-quadruplex RNA binding / perikaryon / microtubule binding / postsynaptic membrane / postsynapse / negative regulation of translation / transmembrane transporter binding / dendritic spine / postsynaptic density / neuron projection / positive regulation of protein phosphorylation / ribonucleoprotein complex / protein heterodimerization activity / axon / DNA repair / mRNA binding / dendrite / neuronal cell body / synapse / chromatin binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | SOLUTION NMR / RMD | ||||||||||||
Authors | Ramos, A. / Hollingworth, D. / Adinolfi, S. / Castets, M. / Kelly, G. / Frenkiel, T.A. / Bardoni, B. / Pastore, A. | ||||||||||||
Citation | Journal: Structure / Year: 2006 Title: The structure of the N-terminal domain of the fragile X mental retardation protein: a platform for protein-protein interaction. Authors: Ramos, A. / Hollingworth, D. / Adinolfi, S. / Castets, M. / Kelly, G. / Frenkiel, T.A. / Bardoni, B. / Pastore, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bkd.cif.gz | 824.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bkd.ent.gz | 703 KB | Display | PDB format |
PDBx/mmJSON format | 2bkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkd ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkd | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15618.598 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FMR1 / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06787 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: NONE |
-Sample preparation
Details | Contents: 10% D2O/90% H2O |
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Sample conditions | Ionic strength: 10 mM / pH: 7.4 / Pressure: 1.0 atm / Temperature: 300.0 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: RMD / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION | |||||||||
NMR ensemble | Conformer selection criteria: LEAST ENERGY AND LEAST RESTRAINT VIOLATION Conformers calculated total number: 100 / Conformers submitted total number: 20 |