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- PDB-7cfd: Drosophila melanogaster Krimper eTud2-AubR15me2 complex -

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Basic information

Entry
Database: PDB / ID: 7cfd
TitleDrosophila melanogaster Krimper eTud2-AubR15me2 complex
Components
  • FI20010p1
  • Protein aubergine
KeywordsGENE REGULATION / piRNA ampilication / gene silencing
Function / homology
Function and homology information


positive regulation of oskar mRNA translation / maternal mRNA clearance / pole cell development / transposable element silencing by piRNA-mediated mRNA destabilization / positive regulation of post-transcriptional gene silencing by RNA / maintenance of pole plasm mRNA location / negative regulation of oskar mRNA translation / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization ...positive regulation of oskar mRNA translation / maternal mRNA clearance / pole cell development / transposable element silencing by piRNA-mediated mRNA destabilization / positive regulation of post-transcriptional gene silencing by RNA / maintenance of pole plasm mRNA location / negative regulation of oskar mRNA translation / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte karyosome formation / regulation of pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / pole plasm assembly / pole cell formation / dorsal appendage formation / transposable element silencing by mRNA destabilization / segmentation / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / global gene silencing by mRNA cleavage / positive regulation of cytoplasmic translational initiation / piRNA processing / transposable element silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mitotic chromosome condensation / P granule / positive regulation of innate immune response / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / oocyte maturation / oogenesis / RNA endonuclease activity / heterochromatin formation / spermatogenesis / defense response to Gram-negative bacterium / mRNA binding / perinuclear region of cytoplasm / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Krimper first tudor domain / : / Tudor domain / Tudor domain profile. / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily ...: / Krimper first tudor domain / : / Tudor domain / Tudor domain profile. / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / Tudor domain / Tudor domain / PAZ domain profile. / PAZ domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tudor domain-containing protein krimp / Protein aubergine
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.704 Å
AuthorsHu, H. / Li, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870755 China
CitationJournal: Nat Commun / Year: 2021
Title: Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex.
Authors: Huang, X. / Hu, H. / Webster, A. / Zou, F. / Du, J. / Patel, D.J. / Sachidanandam, R. / Toth, K.F. / Aravin, A.A. / Li, S.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: FI20010p1
I: Protein aubergine
C: FI20010p1
J: Protein aubergine
K: Protein aubergine
D: FI20010p1
E: FI20010p1
L: Protein aubergine
F: FI20010p1
A: FI20010p1
G: FI20010p1
N: Protein aubergine
H: FI20010p1
M: Protein aubergine
Z: Protein aubergine
O: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)184,75616
Polymers184,75616
Non-polymers00
Water1,33374
1
B: FI20010p1
I: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: FI20010p1
K: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: Protein aubergine
A: FI20010p1


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FI20010p1
O: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: FI20010p1
L: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: FI20010p1
M: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: FI20010p1
N: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: FI20010p1
Z: Protein aubergine


Theoretical massNumber of molelcules
Total (without water)23,0952
Polymers23,0952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.118, 101.365, 191.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FI20010p1 / Krimper


Mass: 21625.797 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: krimp, Dmel\CG15707, KRIMP, Krimp, krimp-RA, mtc, CG15707, Dmel_CG15707
Production host: Escherichia coli (E. coli) / References: UniProt: A1ZAC4
#2: Protein/peptide
Protein aubergine / Protein sting


Mass: 1468.755 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: O76922
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350 and 0.1 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 50060 / % possible obs: 95.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.055 / Rrim(I) all: 0.127 / Net I/σ(I): 12.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 3860 / CC1/2: 0.897 / CC star: 0.972 / Rpim(I) all: 0.284 / Rrim(I) all: 0.588 / % possible all: 75.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.704→48.992 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2904 2518 5.05 %
Rwork0.243 47306 -
obs0.2453 49824 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.14 Å2 / Biso mean: 58.4367 Å2 / Biso min: 22.21 Å2
Refinement stepCycle: final / Resolution: 2.704→48.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12112 0 41 74 12227
Biso mean--65.27 50.86 -
Num. residues----1470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.704-2.75570.44221150.3924193471
2.7557-2.81190.421120.3676215078
2.8119-2.87310.38191240.3507227384
2.8731-2.93990.35991290.3353248991
2.9399-3.01340.37311450.3098258595
3.0134-3.09480.36051350.2835266797
3.0948-3.18590.34021780.2716268399
3.1859-3.28870.29221490.26742723100
3.2887-3.40620.32881420.272271199
3.4062-3.54260.30421270.252275499
3.5426-3.70370.28911490.2396273599
3.7037-3.89890.25111310.2185278099
3.8989-4.14310.30541440.21762727100
4.1431-4.46280.23741330.1974277199
4.4628-4.91150.20331430.19082796100
4.9115-5.62140.25421530.21522788100
5.6214-7.07890.26921510.23862818100
7.0789-48.9920.29411580.238292298

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