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- PDB-4ova: Structure of the two tandem Tudor domains and a new identified KH... -

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Basic information

Entry
Database: PDB / ID: 4ova
TitleStructure of the two tandem Tudor domains and a new identified KH0 domain from human Fragile X Mental Retardation Protein
ComponentsFragile X mental retardation protein 1
KeywordsRNA BINDING PROTEIN / KH DOMAIN / FRAGILE X MENTAL RETARDATION PROTEIN / FMRP / tandem Tudor domains / EUKARYOTIC KH DOMAINS / KH0 domain / protein interaction
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / growth cone filopodium / regulation of translation at presynapse, modulating synaptic transmission / regulation of neuronal action potential / modulation by host of viral RNA genome replication / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / animal organ development ...positive regulation of intracellular transport of viral material / growth cone filopodium / regulation of translation at presynapse, modulating synaptic transmission / regulation of neuronal action potential / modulation by host of viral RNA genome replication / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / animal organ development / negative regulation of voltage-gated calcium channel activity / negative regulation of long-term synaptic depression / dendritic filopodium / regulation of dendritic spine development / RNA strand annealing activity / chromocenter / positive regulation of long-term neuronal synaptic plasticity / filopodium tip / regulation of neurotransmitter secretion / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / N6-methyladenosine-containing RNA reader activity / siRNA binding / poly(A) binding / positive regulation of proteasomal protein catabolic process / membraneless organelle assembly / regulatory ncRNA-mediated gene silencing / sequence-specific mRNA binding / miRNA binding / positive regulation of filopodium assembly / poly(U) RNA binding / intracellular membraneless organelle / glutamate receptor signaling pathway / regulation of alternative mRNA splicing, via spliceosome / positive regulation of dendritic spine development / dynein complex binding / positive regulation of receptor internalization / chromosome, centromeric region / glial cell projection / mRNA transport / mRNA export from nucleus / Cajal body / negative regulation of cytoplasmic translation / translation regulator activity / translation repressor activity / translation initiation factor binding / : / negative regulation of translational initiation / signaling adaptor activity / axon terminus / regulation of mRNA stability / stress granule assembly / RNA splicing / positive regulation of translation / mRNA 3'-UTR binding / cell projection / molecular condensate scaffold activity / cellular response to virus / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / RNA stem-loop binding / mRNA processing / cytoplasmic stress granule / nervous system development / presynapse / presynaptic membrane / ribosome binding / chromosome / growth cone / microtubule binding / G-quadruplex RNA binding / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / negative regulation of translation / protein heterodimerization activity / axon / ribonucleoprotein complex / DNA repair / mRNA binding / synapse / dendrite / chromatin binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, Z.H. / Chen, Z.Z.
CitationJournal: Nat Commun / Year: 2015
Title: The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers
Authors: Hu, Y. / Chen, Z.H. / Fu, Y. / He, Q. / Jiang, L. / Zheng, J. / Gao, Y. / Mei, P. / Chen, Z.Z. / Ren, X.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 8, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,4956
Polymers97,2514
Non-polymers2442
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-31 kcal/mol
Surface area43620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.643, 60.842, 168.856
Angle α, β, γ (deg.)90.00, 122.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24312.723 Da / Num. of mol.: 4 / Fragment: UNP residues 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMR1 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q06787
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.15 Å3/Da / Density % sol: 76.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 39030 / Num. obs: 38927 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 3→3.05 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1920 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
ADSCQuantumdata collection
BALBESphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O8V

3o8v


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 18.037 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1928 5 %RANDOM
Rwork0.2187 ---
obs0.2207 36716 95.82 %-
all-38644 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 225.99 Å2 / Biso mean: 99 Å2 / Biso min: 47.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-5.76 Å2
2--7.98 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6229 0 16 171 6416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196393
X-RAY DIFFRACTIONr_bond_other_d0.0010.025871
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9398695
X-RAY DIFFRACTIONr_angle_other_deg0.796313472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.324.267300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.143151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9611536
X-RAY DIFFRACTIONr_chiral_restr0.0710.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
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_it6.20610.0513194
X-RAY DIFFRACTIONr_mcbond_other6.19710.053192
X-RAY DIFFRACTIONr_mcangle_it10.03115.0543983
X-RAY DIFFRACTIONr_mcangle_other10.0315.0543984
X-RAY DIFFRACTIONr_scbond_it6.08510.4263199
X-RAY DIFFRACTIONr_scbond_other6.08410.4263199
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.96615.4284713
X-RAY DIFFRACTIONr_long_range_B_refined15.10480.0287257
X-RAY DIFFRACTIONr_long_range_B_other15.10680.0137249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 93 -
Rwork0.428 1557 -
obs--55.76 %

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