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- PDB-6opf: Crystal structure of dmNxf2 UBA domain fused with Panoramix helix -

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Basic information

Entry
Database: PDB / ID: 6opf
TitleCrystal structure of dmNxf2 UBA domain fused with Panoramix helix
ComponentsNuclear RNA export factor 2, Panoramix fusion
KeywordsRNA BINDING PROTEIN / Piwi / transposon silencing / heterochromatin formation / piRNA pathway / transcriptional silencing
Function / homology
Function and homology information


piRNA-mediated heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / piRNA binding / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / : / RNA polymerase II transcription repressor complex / protein localization to nuclear periphery / chromatin-protein adaptor activity / poly(A)+ mRNA export from nucleus ...piRNA-mediated heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / piRNA binding / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / : / RNA polymerase II transcription repressor complex / protein localization to nuclear periphery / chromatin-protein adaptor activity / poly(A)+ mRNA export from nucleus / transcription repressor complex / transcription corepressor activity / single-stranded RNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / UBA-like superfamily ...TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Nuclear RNA export factor 2 / Protein panoramix
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, J. / Patel, D.J.
Funding support United States, 3items
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
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.
Authors: Batki, J. / Schnabl, J. / Wang, J. / Handler, D. / Andreev, V.I. / Stieger, C.E. / Novatchkova, M. / Lampersberger, L. / Kauneckaite, K. / Xie, W. / Mechtler, K. / Patel, D.J. / Brennecke, J.
History
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / 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 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear RNA export factor 2, Panoramix fusion
B: Nuclear RNA export factor 2, Panoramix fusion
D: Nuclear RNA export factor 2, Panoramix fusion
F: Nuclear RNA export factor 2, Panoramix fusion


Theoretical massNumber of molelcules
Total (without water)44,3024
Polymers44,3024
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-22 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.890, 72.890, 59.680
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nuclear RNA export factor 2, Panoramix fusion / Protein silencio


Mass: 11075.483 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nxf2, CG4118, Panx, CG9754 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9VV73, UniProt: Q9W2H9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.5 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Sodium citrate pH 5.6, 19% (v/v) Isopropanol, 19% (w/v) PEG 4000, 5% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→45.03 Å / Num. obs: 24962 / % possible obs: 95.7 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3660 / CC1/2: 0.946 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAI

1oai


Resolution: 2→42.981 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.54
RfactorNum. reflection% reflection
Rfree0.2461 1203 4.84 %
Rwork0.2195 --
obs0.2207 24853 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 0 96 2802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072722
X-RAY DIFFRACTIONf_angle_d0.8093680
X-RAY DIFFRACTIONf_dihedral_angle_d3.371646
X-RAY DIFFRACTIONf_chiral_restr0.046440
X-RAY DIFFRACTIONf_plane_restr0.005465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.30651300.28992657X-RAY DIFFRACTION96
2.0801-2.17470.3221260.27162517X-RAY DIFFRACTION92
2.1747-2.28940.28211640.25032642X-RAY DIFFRACTION96
2.2894-2.43280.29081370.2262676X-RAY DIFFRACTION98
2.4328-2.62060.23771300.23092594X-RAY DIFFRACTION94
2.6206-2.88430.28011320.23832674X-RAY DIFFRACTION97
2.8843-3.30150.33321480.24392690X-RAY DIFFRACTION97
3.3015-4.15910.21251230.19282612X-RAY DIFFRACTION94
4.1591-42.99060.16571130.18712588X-RAY DIFFRACTION91

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