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- PDB-7mkk: Crystal structure of Drosophila Panoramix in complex with Sov NTD -

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Basic information

Entry
Database: PDB / ID: 7mkk
TitleCrystal structure of Drosophila Panoramix in complex with Sov NTD
Components
  • Protein panoramix
  • Small ovary, isoform A
KeywordsRNA BINDING/Metal Binding protein / Piwi / transposon silencing / heterochromatin formation / piRNA pathway / transcriptional silencing / RNA BINDING-Metal Binding protein complex
Function / homology
Function and homology information


piRNA-mediated heterochromatin formation / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / transcription repressor complex / negative regulation of gene expression / nucleus
Similarity search - Function
zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Protein panoramix / Small ovary, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWang, J. / Patel, D.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery.
Authors: Andreev, V.I. / Yu, C. / Wang, J. / Schnabl, J. / Tirian, L. / Gehre, M. / Handler, D. / Duchek, P. / Novatchkova, M. / Baumgartner, L. / Meixner, K. / Sienski, G. / Patel, D.J. / Brennecke, J.
History
DepositionApr 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 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
B: Small ovary, isoform A
C: Protein panoramix
A: Small ovary, isoform A
D: Protein panoramix
E: Small ovary, isoform A
F: Protein panoramix
G: Small ovary, isoform A
H: Protein panoramix


Theoretical massNumber of molelcules
Total (without water)49,4138
Polymers49,4138
Non-polymers00
Water1,22568
1
B: Small ovary, isoform A
C: Protein panoramix


Theoretical massNumber of molelcules
Total (without water)12,3532
Polymers12,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-6 kcal/mol
Surface area6120 Å2
MethodPISA
2
A: Small ovary, isoform A
D: Protein panoramix


Theoretical massNumber of molelcules
Total (without water)12,3532
Polymers12,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area6010 Å2
MethodPISA
3
E: Small ovary, isoform A
F: Protein panoramix


Theoretical massNumber of molelcules
Total (without water)12,3532
Polymers12,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area5570 Å2
MethodPISA
4
G: Small ovary, isoform A
H: Protein panoramix


Theoretical massNumber of molelcules
Total (without water)12,3532
Polymers12,3532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-8 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.389, 127.389, 96.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-123-

HOH

21B-125-

HOH

31E-113-

HOH

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Components

#1: Protein
Small ovary, isoform A / Small ovary / isoform B / isoform C


Mass: 9258.927 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: sov, Dmel\CG14438, EM25, fs(1)M105, l(1)6Dc, l(1)EA42, l(1)EM25, CG14438, Dmel_CG14438
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9W3W6
#2: Protein/peptide
Protein panoramix / Protein silencio


Mass: 3094.384 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Panx, CG9754 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9W2H9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16430 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 22.8
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 2329 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.829 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 822 5.01 %
Rwork0.2266 15583 -
obs0.2282 16405 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.91 Å2 / Biso mean: 67.798 Å2 / Biso min: 26.04 Å2
Refinement stepCycle: final / Resolution: 2.5→47.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 0 68 3072
Biso mean---58.72 -
Num. residues----370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.65670.34881410.32552533
2.6567-2.86180.341210.31032535
2.8618-3.14970.36991240.30262574
3.1497-3.60530.28651410.25392565
3.6053-4.54180.23361340.19522620
4.5418-47.8290.2161610.19122756

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