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- PDB-3nti: Crystal structure of Tudor and Aubergine [R15(me2s)] complex -

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Basic information

Entry
Database: PDB / ID: 3nti
TitleCrystal structure of Tudor and Aubergine [R15(me2s)] complex
Components
  • Maternal protein tudorMother
  • peptide from Aubergine
KeywordsTRANSCRIPTION / Tudor domain / OB-fold / germ cell formation
Function / homology
Function and homology information


positive regulation of oskar mRNA translation / pole cell development / maintenance of pole plasm mRNA location / positive regulation of post-transcriptional gene silencing by RNA / regulation of oskar mRNA translation / retrotransposon silencing by mRNA destabilization / P granule assembly / pole plasm protein localization / oocyte karyosome formation / methylation-dependent protein binding ...positive regulation of oskar mRNA translation / pole cell development / maintenance of pole plasm mRNA location / positive regulation of post-transcriptional gene silencing by RNA / regulation of oskar mRNA translation / retrotransposon silencing by mRNA destabilization / P granule assembly / pole plasm protein localization / oocyte karyosome formation / methylation-dependent protein binding / pole plasm / secondary piRNA processing / regulation of pole plasm oskar mRNA localization / P granule organization / piRNA binding / pole plasm assembly / segmentation / RNA endonuclease activity, producing 5'-phosphomonoesters / pole cell formation / dorsal appendage formation / piRNA processing / global gene silencing by mRNA cleavage / intracellular mRNA localization / regulatory ncRNA-mediated post-transcriptional gene silencing / retrotransposon silencing / oocyte maturation / regulatory ncRNA-mediated gene silencing / P granule / positive regulation of innate immune response / mitotic chromosome condensation / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / oogenesis / germ cell development / heterochromatin formation / RNA endonuclease activity / spermatogenesis / defense response to Gram-negative bacterium / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #790 / Tudor domain / Tudor domain profile. / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #790 / Tudor domain / Tudor domain profile. / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein aubergine / Maternal protein tudor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, H.P. / Huang, Y. / Li, Z.Z. / Gong, W.M. / Xu, R.M.
CitationJournal: Genes Dev. / Year: 2010
Title: Structural basis for methylarginine-dependent recognition of Aubergine by Tudor
Authors: Liu, H.P. / Wang, J.Y. / Huang, Y. / Li, Z.Z. / Gong, W.M. / Lehmann, R. / Xu, R.M.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maternal protein tudor
C: peptide from Aubergine


Theoretical massNumber of molelcules
Total (without water)21,0372
Polymers21,0372
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-4 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.790, 48.790, 152.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Maternal protein tudor / Mother


Mass: 19568.021 Da / Num. of mol.: 1 / Fragment: the last extended Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: tud / Plasmid: pET-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P25823
#2: Protein/peptide peptide from Aubergine / / Aub[R15(me2s)]


Mass: 1468.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in drosophila. / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: O76922
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG8000, 0.2M sodium acetate trihytrate, 0.1M sodium cacodylate trihydrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 5026 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4 / Num. unique all: 484 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTK

3ntk


Resolution: 2.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8147 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2761 517 10.4 %
Rwork0.2386 --
obs-4979 99.7 %
Solvent computationBsol: 48.3909 Å2
Displacement parametersBiso max: 100 Å2 / Biso mean: 69.2995 Å2 / Biso min: 38.22 Å2
Baniso -1Baniso -2Baniso -3
1-5.898 Å20 Å20 Å2
2--5.898 Å20 Å2
3----11.797 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 0 18 1360
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0081.5
X-RAY DIFFRACTIONc_angle_deg1.582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.90.3492400.3124430470
2.9-3.020.3346560.2796431487
3.02-3.150.358590.2959414473
3.15-3.320.3562470.2563439486
3.32-3.530.2851470.2468442489
3.53-3.80.2898520.2368446498
3.8-4.180.2477520.2305436488
4.18-4.790.221620.1737442504
4.79-6.030.2535520.2067466518
6.03-500.2975500.2366516566
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_sa2.param
X-RAY DIFFRACTION2water_rep.param

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