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- PDB-2cpq: Solution structure of the N-terminal KH domain of human FXR1 -

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Entry
Database: PDB / ID: 2cpq
TitleSolution structure of the N-terminal KH domain of human FXR1
ComponentsFragile X mental retardation syndrome related protein 1, isoform b'
KeywordsRNA BINDING PROTEIN / KH domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of mRNA catabolic process / regulation of translation at presynapse, modulating synaptic transmission / skeletal muscle organ development / positive regulation of miRNA-mediated gene silencing / animal organ development / RNA strand annealing activity / nuclear pore localization / regulation of circadian sleep/wake cycle, sleep / nuclear pore complex assembly / positive regulation of long-term neuronal synaptic plasticity ...negative regulation of mRNA catabolic process / regulation of translation at presynapse, modulating synaptic transmission / skeletal muscle organ development / positive regulation of miRNA-mediated gene silencing / animal organ development / RNA strand annealing activity / nuclear pore localization / regulation of circadian sleep/wake cycle, sleep / nuclear pore complex assembly / positive regulation of long-term neuronal synaptic plasticity / membraneless organelle assembly / dentate gyrus development / costamere / mRNA 3'-UTR AU-rich region binding / intracellular membraneless organelle / muscle organ development / mRNA destabilization / negative regulation of tumor necrosis factor production / regulation of neurogenesis / negative regulation of long-term synaptic potentiation / spermatid development / mRNA transport / translation regulator activity / regulation of synaptic transmission, glutamatergic / regulation of mRNA stability / mRNA 3'-UTR binding / positive regulation of translation / molecular condensate scaffold activity / negative regulation of inflammatory response / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / Signaling by BRAF and RAF1 fusions / nuclear envelope / presynapse / dendritic spine / negative regulation of translation / ribosome / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / nucleolus / apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Fragile X-related 1 protein, C-terminal region 3 / : / : / : / : / : / Fragile X-related 1 protein C-terminal region 3 / Fragile X-related protein 1, C-terminal region 1 / Fragile X-related 1 protein C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core ...Fragile X-related 1 protein, C-terminal region 3 / : / : / : / : / : / Fragile X-related 1 protein C-terminal region 3 / Fragile X-related protein 1, C-terminal region 1 / Fragile X-related 1 protein 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 / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein FXR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dyanamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the N-terminal KH domain of human FXR1
Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fragile X mental retardation syndrome related protein 1, isoform b'


Theoretical massNumber of molelcules
Total (without water)9,5831
Polymers9,5831
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Fragile X mental retardation syndrome related protein 1, isoform b'


Mass: 9582.562 Da / Num. of mol.: 1 / Fragment: KH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: FXR1 / Plasmid: p040621-02 / References: UniProt: P51114

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.20mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801/20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.925Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dyanamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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