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- PDB-3kuf: The Crystal Structure of the Tudor Domains from FXR1 -

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Basic information

Entry
Database: PDB / ID: 3kuf
TitleThe Crystal Structure of the Tudor Domains from FXR1
ComponentsFragile X mental retardation syndrome-related protein 1
KeywordsPROTEIN BINDING / TANDEM TUDOR / Structural Genomics Consortium / RNA-binding Fragile X mental retardation syndrome-related protein 1 / SGC
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 / dendritic filopodium / nuclear pore localization / RNA strand annealing activity / regulation of circadian sleep/wake cycle, sleep ...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 / dendritic filopodium / nuclear pore localization / RNA strand annealing activity / regulation of circadian sleep/wake cycle, sleep / positive regulation of long-term neuronal synaptic plasticity / nuclear pore complex assembly / regulation of filopodium assembly / mRNA 3'-UTR AU-rich region binding / non-membrane-bounded organelle assembly / dentate gyrus development / costamere / muscle organ development / intracellular non-membrane-bounded organelle / dendritic spine neck / mRNA destabilization / regulation of alternative mRNA splicing, via spliceosome / negative regulation of tumor necrosis factor production / negative regulation of long-term synaptic potentiation / spermatid development / regulation of neurogenesis / mRNA transport / translation regulator activity / regulation of synaptic transmission, glutamatergic / regulation of mRNA stability / molecular condensate scaffold activity / mRNA 3'-UTR binding / positive regulation of translation / cytoplasmic ribonucleoprotein granule / negative regulation of inflammatory response / cytoplasmic stress granule / Signaling by BRAF and RAF1 fusions / presynapse / nuclear envelope / growth cone / postsynaptic density / negative regulation of translation / ribosome / neuron projection / positive regulation of protein phosphorylation / protein heterodimerization activity / neuronal cell body / glutamatergic synapse / apoptotic process / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / membrane / nucleus / cytoplasm / cytosol
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 / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / RNA-binding protein FXR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBian, C. / Guo, Y.H. / Adams-Cioaba, M.A. / Mackenzie, F. / Kozieradzki, I. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Bian, C. / Guo, Y.H. / Adams-Cioaba, M.A. / Mackenzie, F. / Kozieradzki, I. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the Tudor domains from Fragile X mental retardation syndrome-related protein 1
Authors: Guo, Y.H. / Adams-Cioaba, M. / Bian, C.B. / Min, J.R. / Structural Genomics Consortium (SGC)
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Fragile X mental retardation syndrome-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8607
Polymers15,2451
Non-polymers6156
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.102, 73.102, 94.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Fragile X mental retardation syndrome-related protein 1 / hFXR1p


Mass: 15245.146 Da / Num. of mol.: 1 / Fragment: UNP residues 2-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXR1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P51114
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.38 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorDate: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→26.29 Å / Num. obs: 5131

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H8Z

3h8z


Resolution: 2.7→26.29 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 43.11 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R: 0.646 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29577 237 4.6 %RANDOM
Rwork0.24767 ---
obs0.24986 4891 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 38 26 957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.881.9721273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3845104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88624.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.88215150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.414157
X-RAY DIFFRACTIONr_chiral_restr0.0710.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021713
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7971.5538
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4652877
X-RAY DIFFRACTIONr_scbond_it4.4463409
X-RAY DIFFRACTIONr_scangle_it7.5364.5396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.705→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 19 -
Rwork0.301 366 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 21.1047 Å / Origin y: 21.1216 Å / Origin z: -0.6962 Å
111213212223313233
T0.0346 Å2-0.0048 Å2-0.0145 Å2-0.0806 Å20.0096 Å2--0.0822 Å2
L0.7758 °20.9399 °20.6217 °2-1.7532 °21.2755 °2--1.5487 °2
S0.0351 Å °-0.0434 Å °0.0121 Å °-0.0819 Å °-0.0041 Å °0.0189 Å °-0.077 Å °-0.2046 Å °-0.031 Å °

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