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- PDB-4qw2: FMRP N-terminal domain (R138Q) -

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Basic information

Entry
Database: PDB / ID: 4qw2
TitleFMRP N-terminal domain (R138Q)
ComponentsFragile X mental retardation protein 1FMR1
KeywordsTRANSLATION / FMRP / FMR1 / Tandem Agenet / KH / Histone binding / RNA binding / nuclear
Function / homology
Function and homology information


regulation of translation at presynapse, modulating synaptic transmission / positive regulation of intracellular transport of viral material / 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 ...regulation of translation at presynapse, modulating synaptic transmission / positive regulation of intracellular transport of viral material / 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 / regulation of neurotransmitter secretion / filopodium tip / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / non-membrane-bounded organelle assembly / positive regulation of proteasomal protein catabolic process / N6-methyladenosine-containing RNA reader activity / poly(A) binding / siRNA binding / regulatory ncRNA-mediated gene silencing / glutamate receptor signaling pathway / sequence-specific mRNA binding / poly(U) RNA binding / miRNA binding / positive regulation of filopodium assembly / dynein complex binding / positive regulation of dendritic spine development / dendritic spine neck / intracellular non-membrane-bounded organelle / 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 / Cajal body / mRNA export from nucleus / axon terminus / signaling adaptor activity / stress granule assembly / RNA stem-loop binding / 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 stress granule / cytoplasmic ribonucleoprotein granule / 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 / neuron projection / ribonucleoprotein complex / positive regulation of protein phosphorylation / protein heterodimerization activity / axon / DNA repair / mRNA binding / synapse / dendrite / chromatin binding / nucleolus / 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 / Type-1 KH domain profile. / SH3 type barrels. - #140 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
LEAD (II) ION / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.989 Å
AuthorsMyrick, L.K. / Hashimoto, H. / Cheng, X. / Warren, S.T.
CitationJournal: Hum.Mol.Genet. / Year: 2015
Title: Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain.
Authors: Myrick, L.K. / Hashimoto, H. / Cheng, X. / Warren, S.T.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fragile X mental retardation protein 1
B: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0344
Polymers49,7652
Non-polymers2692
Water19811
1
A: Fragile X mental retardation protein 1


Theoretical massNumber of molelcules
Total (without water)24,8821
Polymers24,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1523
Polymers24,8821
Non-polymers2692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.087, 89.087, 121.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fragile X mental retardation protein 1 / FMR1 / FMRP / Protein FMR-1


Mass: 24882.270 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-213) / Mutation: R138Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMR1 / Plasmid: pET28b-His-sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q06787
#2: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25-30% PEG5000 MME, 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 5 mM CH3Pb, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9439 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2014
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9439 Å / Relative weight: 1
ReflectionResolution: 2.989→24.901 Å / Num. all: 10452 / Num. obs: 10425 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.989-3.28896.50.712.9751100
3.2889-3.76341100
3.7634-4.73611100
4.7361-24.90171100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O8V

3o8v


Resolution: 2.989→24.901 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 522 5.01 %RANDOM
Rwork0.2265 ---
obs0.2293 10425 99.88 %-
all-10452 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.989→24.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 5 11 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033153
X-RAY DIFFRACTIONf_angle_d0.6514305
X-RAY DIFFRACTIONf_dihedral_angle_d13.2681102
X-RAY DIFFRACTIONf_chiral_restr0.025489
X-RAY DIFFRACTIONf_plane_restr0.003559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.989-3.28890.29771270.26542402X-RAY DIFFRACTION100
3.2889-3.76340.35521280.25072440X-RAY DIFFRACTION100
3.7634-4.73610.28191290.20872468X-RAY DIFFRACTION100
4.7361-24.90170.24421380.21712593X-RAY DIFFRACTION100

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