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- PDB-2bkd: Structure of the N-terminal domain of Fragile X Mental Retardatio... -

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Basic information

Entry
Database: PDB / ID: 2bkd
TitleStructure of the N-terminal domain of Fragile X Mental Retardation Protein
ComponentsFragile X messenger ribonucleoprotein 1
KeywordsNUCLEAR PROTEIN / FMRP / PROTEIN-PROTEIN INTERACTION / MRNA TRANSPORT
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / regulation of mRNA metabolic process / regulation of translation at presynapse, modulating synaptic transmission / dendritic filopodium / negative regulation of voltage-gated calcium channel activity / host-mediated perturbation of viral RNA genome replication / positive regulation of miRNA-mediated gene silencing / negative regulation of synaptic vesicle exocytosis / poly(G) binding / negative regulation of miRNA-mediated gene silencing ...positive regulation of intracellular transport of viral material / regulation of mRNA metabolic process / regulation of translation at presynapse, modulating synaptic transmission / dendritic filopodium / negative regulation of voltage-gated calcium channel activity / host-mediated perturbation of viral RNA genome replication / positive regulation of miRNA-mediated gene silencing / negative regulation of synaptic vesicle exocytosis / poly(G) binding / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / negative regulation of long-term synaptic depression / regulation of neuronal action potential / intracellular membraneless organelle / animal organ development / histone H3 reader activity / RNA strand annealing activity / regulation of dendritic spine development / chromocenter / filopodium tip / positive regulation of long-term neuronal synaptic plasticity / regulation of neurotransmitter secretion / regulation of filopodium assembly / N6-methyladenosine-containing RNA reader activity / poly(A) binding / membraneless organelle assembly / siRNA binding / sequence-specific mRNA binding / growth cone filopodium / positive regulation of filopodium assembly / regulatory ncRNA-mediated gene silencing / positive regulation of proteasomal protein catabolic process / miRNA binding / poly(U) RNA binding / positive regulation of dendritic spine development / regulation of alternative mRNA splicing, via spliceosome / glutamate receptor signaling pathway / dynein complex binding / positive regulation of receptor internalization / chromosome, centromeric region / glial cell projection / mRNA transport / Cajal body / mRNA export from nucleus / cell projection / negative regulation of cytoplasmic translation / regulation of mRNA stability / translation regulator activity / translation repressor activity / negative regulation of translational initiation / signaling adaptor activity / translation initiation factor binding / RNA splicing / excitatory synapse / axon terminus / stress granule assembly / positive regulation of translation / cellular response to virus / mRNA 3'-UTR binding / molecular condensate scaffold activity / RNA stem-loop binding / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / mRNA processing / cytoplasmic stress granule / nervous system development / presynapse / chromosome / growth cone / ribosome binding / presynaptic membrane / G-quadruplex RNA binding / microtubule binding / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / postsynapse / postsynaptic density / negative regulation of translation / neuron projection / protein heterodimerization activity / ribonucleoprotein complex / axon / DNA repair / mRNA binding / chromatin binding / nucleolus / dendrite / synapse / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain ...Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. / Agenet-like domain / Agenet domain / KH domain / K Homology domain, type 1 / SH3 type barrels. - #140 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / SH3 type barrels. / K Homology domain / K homology RNA-binding domain / Roll / Mainly Beta
Similarity search - Domain/homology
Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / RMD
AuthorsRamos, A. / Hollingworth, D. / Adinolfi, S. / Castets, M. / Kelly, G. / Frenkiel, T.A. / Bardoni, B. / Pastore, A.
CitationJournal: 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
DepositionFeb 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 28, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / citation / entity_src_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 3.0Feb 1, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nmr_software / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_torsion / struct_conn / struct_ref
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_software.name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_torsion.auth_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 3.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond / pdbx_entry_details

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Structure visualization

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Assembly

Deposited unit
N: Fragile X messenger ribonucleoprotein 1


Theoretical massNumber of molelcules
Total (without water)15,6191
Polymers15,6191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST ENERGY AND LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein Fragile X messenger ribonucleoprotein 1 / Fragile X messenger ribonucleoprotein / FMRP / Protein FMR-1


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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-NOESY
12113C-NOESY
131HNCO
141HNCA
151HN(CO)CACB
161HN(CA)CB
NMR detailsText: NONE

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Sample preparation

DetailsContents: 10% D2O/90% H2O
Sample conditionsIonic strength: 10 mM / pH: 7.4 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHC.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJrefinement
XEASYstructure solution
RefinementMethod: RMD / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION
NMR ensembleConformer selection criteria: LEAST ENERGY AND LEAST RESTRAINT VIOLATION
Conformers calculated total number: 100 / Conformers submitted total number: 20

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