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- PDB-2fmr: KH1 FROM THE FRAGILE X PROTEIN FMR1, NMR, 18 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 2fmr
TitleKH1 FROM THE FRAGILE X PROTEIN FMR1, NMR, 18 STRUCTURES
ComponentsFMR1 PROTEIN
KeywordsRNA BINDING PROTEIN / FMR1 / FRAGILE X / MODULAR PROTEINS / RNA-BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / regulation of translation at presynapse, modulating synaptic transmission / 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 / regulation of translation at presynapse, modulating synaptic transmission / 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 / animal organ development / negative regulation of voltage-gated calcium channel activity / dendritic filopodium / RNA strand annealing activity / chromocenter / regulation of dendritic spine development / positive regulation of long-term neuronal synaptic plasticity / filopodium tip / regulation of neurotransmitter secretion / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / non-membrane-bounded organelle assembly / regulatory ncRNA-mediated gene silencing / poly(A) binding / positive regulation of proteasomal protein catabolic process / N6-methyladenosine-containing RNA reader activity / siRNA binding / poly(U) RNA binding / sequence-specific mRNA binding / glutamate receptor signaling pathway / miRNA binding / positive regulation of filopodium assembly / intracellular non-membrane-bounded organelle / dynein complex binding / positive regulation of dendritic spine development / dendritic spine neck / regulation of alternative mRNA splicing, via spliceosome / glial cell projection / positive regulation of receptor internalization / chromosome, centromeric region / mRNA transport / translation regulator activity / negative regulation of cytoplasmic translation / mRNA export from nucleus / signaling adaptor activity / stress granule assembly / axon terminus / Cajal body / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / regulation of mRNA stability / methylated histone binding / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / cell projection / positive regulation of translation / mRNA processing / cellular response to virus / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / RNA stem-loop binding / presynapse / ribosome binding / presynaptic membrane / chromosome / nervous system development / growth cone / G-quadruplex RNA binding / postsynapse / microtubule binding / postsynaptic membrane / perikaryon / transmembrane transporter binding / dendritic spine / postsynaptic density / negative regulation of translation / ribonucleoprotein complex / neuron projection / positive regulation of protein phosphorylation / protein heterodimerization activity / axon / DNA repair / mRNA binding / synapse / chromatin binding / dendrite / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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 / 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
Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMusco, G. / Kharrat, A. / Stier, G. / Fraternali, F. / Gibson, T.J. / Nilges, M. / Pastore, A.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome.
Authors: Musco, G. / Kharrat, A. / Stier, G. / Fraternali, F. / Gibson, T.J. / Nilges, M. / Pastore, A.
History
DepositionOct 6, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMR1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,2711
Polymers7,2711
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)18 / 50ENERGY, RMS
Representative

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Components

#1: Protein FMR1 PROTEIN / KH1


Mass: 7271.123 Da / Num. of mol.: 1 / Fragment: FIRST KH DOMAIN RESIDUES 216 - 280
Source method: isolated from a genetically manipulated source
Details: MODULE FROM THE KH FAMILY / Source: (gene. exp.) Homo sapiens (human)
Description: HUMAN CDNA SEQUENCE CODING THE FIRST DOMAIN OF FMR WAS PCR AMPLIFIED AND SUB-CLONED INTO A PET9 DERIVED PLASMID VECTOR WITH C-TERMINAL HIS-TAG
Cell line: BL21 / Cellular location: CYTOPLASM / Gene: FMR1 / Plasmid: PET9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06787

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131NOESY HSQC
141HMQC-J

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
ARIAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JNRL CITATION. ARIA (NILGES) ALSO WAS USED.
NMR ensembleConformer selection criteria: ENERGY, RMS / Conformers calculated total number: 50 / Conformers submitted total number: 18

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