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- PDB-3o8v: Crystal Structure of the Tudor Domains from FXR1 -

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Basic information

Entry
Database: PDB / ID: 3o8v
TitleCrystal Structure of the Tudor Domains from FXR1
ComponentsFragile X mental retardation syndrome-related protein 1
KeywordsPROTEIN BINDING / Structural Genomics Consortium / SGC / Tandem Tudor / RNA-binding
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
RNA-binding protein FXR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLam, R. / Guo, Y.H. / Adams-Cioaba, M. / Bian, C.B. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Lam, R. / Guo, Y.H. / Adams-Cioaba, M. / Bian, C.B. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2.
Authors: Adams-Cioaba, M.A. / Guo, Y. / Bian, C. / Amaya, M.F. / Lam, R. / Wasney, G.A. / Vedadi, M. / Xu, C. / Min, J.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)15,2451
Polymers15,2451
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.857, 71.857, 94.055
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: residues 2-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXR1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: P51114
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.4M Ammonium Sulfate, 0.1M HEPES pH 6.8, 0.25 M NaCl, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97904 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 11, 2010 / Details: Double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.941
11K, H, -L20.059
ReflectionResolution: 2.5→50 Å / Num. obs: 6291 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.074 / Χ2: 3.016 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.593.90.5496411.031100
2.59-2.6940.4266261.011100
2.69-2.823.90.3226131.117100
2.82-2.963.90.2366341.323100
2.96-3.1540.1486301.508100
3.15-3.393.90.0876271.93100
3.39-3.7340.0666381.902100
3.73-4.2740.0646291.636100
4.27-5.3840.0566254.988100
5.38-5040.06762813.67499.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 35.93 Å / FOM acentric: 0.346 / FOM centric: 0 / Reflection acentric: 6265 / Reflection centric: 0
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.535.9362650
ANO_10.59502.535.9362610
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_19.66-35.93001050
ISO_16.95-9.66001860
ISO_15.71-6.95002230
ISO_14.96-5.71002870
ISO_14.45-4.96003090
ISO_14.07-4.45003440
ISO_13.77-4.07003710
ISO_13.53-3.77004100
ISO_13.33-3.53004260
ISO_13.16-3.33004530
ISO_13.01-3.16004570
ISO_12.88-3.01004930
ISO_12.77-2.88005260
ISO_12.67-2.77005510
ISO_12.58-2.67005410
ISO_12.5-2.58005830
ANO_19.66-35.930.28701030
ANO_16.95-9.660.22901860
ANO_15.71-6.950.27402230
ANO_14.96-5.710.36602870
ANO_14.45-4.960.40203090
ANO_14.07-4.450.58103440
ANO_13.77-4.070.67103700
ANO_13.53-3.770.64904100
ANO_13.33-3.530.73404260
ANO_13.16-3.330.78704530
ANO_13.01-3.160.87504570
ANO_12.88-3.010.92904930
ANO_12.77-2.880.94905260
ANO_12.67-2.770.97805510
ANO_12.58-2.670.99405410
ANO_12.5-2.581.00205820
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-24.19958.23229.627SE81.050.91
2-24.81658.45939.46SE72.420.88
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
9.66-35.930.61101050
6.95-9.660.64901860
5.71-6.950.61702230
4.96-5.710.55602870
4.45-4.960.55303090
4.07-4.450.47303440
3.77-4.070.403710
3.53-3.770.4504100
3.33-3.530.41104260
3.16-3.330.37804530
3.01-3.160.30704570
2.88-3.010.27404930
2.77-2.880.23805260
2.67-2.770.18905510
2.58-2.670.15705410
2.5-2.580.13705830
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 6263
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.76-10055.60.847503
4.6-5.76510.934511
4.01-4.657.80.937502
3.65-4.0157.50.909502
3.39-3.6558.60.898502
3.19-3.3967.40.889511
3.03-3.1972.80.886511
2.89-3.0375.90.871507
2.78-2.89810.794505
2.68-2.7876.70.826503
2.6-2.6882.20.809509
2.5-2.685.80.738697

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6.1phasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→35.93 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.232 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.86 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY, The data is hemohedral twinning with twinning operators: ((H, K, L),(K, H, -L) and corresponding twinned fractions: 0.941, 0.059.
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 288 4.6 %RANDOM
Rwork0.2183 ---
obs0.2201 6288 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 141.67 Å2 / Biso mean: 71.1447 Å2 / Biso min: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-25.81 Å20 Å20 Å2
2--25.81 Å20 Å2
3----51.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 0 1 806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022826
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9331125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.546598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8323.8142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.62915116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.117156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.496-2.5610.468210.21743746099.565
2.561-2.630.413260.29242945699.781
2.63-2.7060.396300.305411441100
2.706-2.7890.371290.297384413100
2.789-2.880.30880.313431439100
2.88-2.980.199180.286349367100
2.98-3.0920.339210.28371392100
3.092-3.2170.297140.267366380100
3.217-3.3590.332220.233338360100
3.359-3.5210.405140.25322336100
3.521-3.710.2450.23335340100
3.71-3.9320.29290.212295304100
3.932-4.20.202140.175260274100
4.2-4.5320.284120.168265277100
4.532-4.9560.2150.165242247100
4.956-5.5280.148100.191217227100
5.528-6.3580.11860.179198204100
6.358-7.7270.346120.204152164100
7.727-10.6830.1780.20512813799.27
10.683-35.9310.11940.268707796.104

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