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- PDB-5ygd: Crystal structure of Drosophila melanogaster Papi extended Tudor ... -

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Basic information

Entry
Database: PDB / ID: 5ygd
TitleCrystal structure of Drosophila melanogaster Papi extended Tudor domain (D287A) in complex with Piwi N-terminal R10me2s peptide
Components
  • ASP-GLN-GLY-ARG-GLY-ARG-2MR-ARG-PRO-LEU-ASN
  • GH18329p
KeywordsPROTEIN BINDING / piRNA / complex / extended Tudor domain
Function / homology
Function and homology information


Yb body / primary piRNA processing / male germ-line stem cell asymmetric division / germarium-derived oocyte fate determination / P granule organization / pole cell formation / post-transcriptional gene silencing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / female germ-line stem cell asymmetric division ...Yb body / primary piRNA processing / male germ-line stem cell asymmetric division / germarium-derived oocyte fate determination / P granule organization / pole cell formation / post-transcriptional gene silencing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / female germ-line stem cell asymmetric division / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / piRNA processing / transposable element silencing by heterochromatin formation / germ-line stem cell population maintenance / chromocenter / transposable element silencing / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / germ cell nucleus / oogenesis / heterochromatin / RNA endonuclease activity / euchromatin / chromatin DNA binding / heterochromatin formation / spermatogenesis / chromatin / protein-containing complex / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / Piwi, N-terminal domain / Tudor domain / Tudor domain profile. / KH domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi ...: / : / Piwi, N-terminal domain / Tudor domain / Tudor domain profile. / KH domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / K Homology domain, type 1 / PAZ domain superfamily / PAZ / PAZ domain / Tudor domain / Tudor domain / PAZ domain profile. / PAZ domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / SH3 type barrels. / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein piwi / Tudor and KH domain-containing protein homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsZhang, Y.H. / Huang, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural insights into the sequence-specific recognition of Piwi byDrosophilaPapi
Authors: Zhang, Y. / Liu, W. / Li, R. / Gu, J. / Wu, P. / Peng, C. / Ma, J. / Wu, L. / Yu, Y. / Huang, Y.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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: GH18329p
D: ASP-GLN-GLY-ARG-GLY-ARG-2MR-ARG-PRO-LEU-ASN


Theoretical massNumber of molelcules
Total (without water)26,4682
Polymers26,4682
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-2 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.472, 72.472, 50.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein GH18329p / Papi / isoform A / isoform B / isoform C / isoform D


Mass: 25112.564 Da / Num. of mol.: 1 / Fragment: UNP residues 259-479 / Mutation: D287A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: papi, Dmel\CG7082, PAPI, Papi, CG7082, Dmel_CG7082 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VQ91
#2: Protein/peptide ASP-GLN-GLY-ARG-GLY-ARG-2MR-ARG-PRO-LEU-ASN


Mass: 1355.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Piwi / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VKM1*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Sodium malonate pH7.0, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 37809 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDR

3fdr


Resolution: 1.551→29.403 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2297 1999 5.29 %
Rwork0.2032 --
obs0.2047 37809 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.551→29.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 0 293 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071814
X-RAY DIFFRACTIONf_angle_d1.1042465
X-RAY DIFFRACTIONf_dihedral_angle_d12.418671
X-RAY DIFFRACTIONf_chiral_restr0.043278
X-RAY DIFFRACTIONf_plane_restr0.004313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5507-1.58940.29441360.27592435X-RAY DIFFRACTION96
1.5894-1.63240.27381410.26282583X-RAY DIFFRACTION100
1.6324-1.68040.29021390.24942525X-RAY DIFFRACTION100
1.6804-1.73470.25331420.24532557X-RAY DIFFRACTION100
1.7347-1.79670.25711450.23462543X-RAY DIFFRACTION100
1.7967-1.86860.29161430.23062559X-RAY DIFFRACTION100
1.8686-1.95360.25691410.23322545X-RAY DIFFRACTION100
1.9536-2.05660.27541430.2242546X-RAY DIFFRACTION100
2.0566-2.18540.2631460.21422568X-RAY DIFFRACTION100
2.1854-2.35410.24451420.22212572X-RAY DIFFRACTION100
2.3541-2.59080.24921450.22562572X-RAY DIFFRACTION100
2.5908-2.96540.25141450.21082554X-RAY DIFFRACTION100
2.9654-3.73490.24851430.18972603X-RAY DIFFRACTION100
3.7349-29.40870.15271480.16232648X-RAY DIFFRACTION100

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