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- PDB-7cfc: Drosophila melanogaster Krimper eTud1-Ago3 complex -

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Basic information

Entry
Database: PDB / ID: 7cfc
TitleDrosophila melanogaster Krimper eTud1-Ago3 complex
Components
  • FI20010p1
  • Protein argonaute-3
KeywordsGENE REGULATION / piRNA ampilication / gene silencing
Function / homology
Function and homology information


extrinsic component of mitochondrial outer membrane / transposable element silencing by piRNA-mediated mRNA destabilization / negative regulation of oskar mRNA translation / oocyte karyosome formation / oocyte dorsal/ventral axis specification / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / P granule ...extrinsic component of mitochondrial outer membrane / transposable element silencing by piRNA-mediated mRNA destabilization / negative regulation of oskar mRNA translation / oocyte karyosome formation / oocyte dorsal/ventral axis specification / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / 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. / SNase-like, OB-fold superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Tudor domain-containing protein krimp / Protein argonaute-3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FI20010p1
B: FI20010p1
C: FI20010p1
D: FI20010p1
E: FI20010p1
F: Protein argonaute-3
G: Protein argonaute-3
H: Protein argonaute-3
I: Protein argonaute-3


Theoretical massNumber of molelcules
Total (without water)142,7469
Polymers142,7469
Non-polymers00
Water5,188288
1
A: FI20010p1
F: Protein argonaute-3


Theoretical massNumber of molelcules
Total (without water)28,9042
Polymers28,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-5 kcal/mol
Surface area9280 Å2
MethodPISA
2
B: FI20010p1
G: Protein argonaute-3


Theoretical massNumber of molelcules
Total (without water)28,9042
Polymers28,9042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area9420 Å2
MethodPISA
3
C: FI20010p1
H: Protein argonaute-3


Theoretical massNumber of molelcules
Total (without water)28,9042
Polymers28,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area9570 Å2
MethodPISA
4
D: FI20010p1
I: Protein argonaute-3


Theoretical massNumber of molelcules
Total (without water)28,9042
Polymers28,9042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5 kcal/mol
Surface area9510 Å2
MethodPISA
5
E: FI20010p1


Theoretical massNumber of molelcules
Total (without water)27,1311
Polymers27,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.464, 88.464, 181.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
FI20010p1 / Krimper


Mass: 27130.713 Da / Num. of mol.: 5
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 argonaute-3 / Ago3


Mass: 1773.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q7PLK0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 1.5M lithium sulfate

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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: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 61822 / % possible obs: 99.3 % / Redundancy: 4.3 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.05 / Rrim(I) all: 0.107 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 6092 / CC1/2: 0.613 / CC star: 0.872 / Rpim(I) all: 0.467 / % possible all: 98.6

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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: 2.4→47.513 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 3073 4.98 %
Rwork0.2342 58648 -
obs0.2354 61721 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.14 Å2 / Biso mean: 56.0044 Å2 / Biso min: 27.32 Å2
Refinement stepCycle: final / Resolution: 2.4→47.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7227 0 0 288 7515
Biso mean---52.88 -
Num. residues----915
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.43740.29351200.286268498
2.4374-2.47730.30851820.2948258198
2.4773-2.520.35461360.2973266299
2.52-2.56590.30971030.30942674100
2.5659-2.61520.3487960.301274499
2.6152-2.66860.3504950.2939270099
2.6686-2.72660.31411650.28282638100
2.7266-2.790.30471550.2627265099
2.79-2.85980.30171710.2732648100
2.8598-2.93710.28151560.2682685100
2.9371-3.02350.33441220.27072664100
3.0235-3.12110.30241930.26752628100
3.1211-3.23260.2772920.2448267199
3.2326-3.3620.24341720.23142687100
3.362-3.5150.24951270.22782691100
3.515-3.70020.25521420.2178267199
3.7002-3.93190.24821660.22282628100
3.9319-4.23540.22871380.20092728100
4.2354-4.66130.1981220.18512693100
4.6613-5.3350.1971540.2007263099
5.335-6.71850.21711320.2459268199
6.7185-47.5130.30451340.225261097

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