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- PDB-6mrk: Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15 -

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Basic information

Entry
Database: PDB / ID: 6mrk
TitleCrystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15
Components
  • NTF2-related export protein
  • Nuclear RNA export factor 2
KeywordsRNA BINDING PROTEIN / Piwi / transposon silencing / heterochromatin formation / piRNA pathway / transcriptional silencing
Function / homology
Function and homology information


Transport of Mature mRNA derived from an Intron-Containing Transcript / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / nuclear pore central transport channel / protein localization to nuclear periphery / chromatin-protein adaptor activity / poly(A)+ mRNA export from nucleus / transcription repressor complex / negative regulation of innate immune response / transcription corepressor activity ...Transport of Mature mRNA derived from an Intron-Containing Transcript / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / nuclear pore central transport channel / protein localization to nuclear periphery / chromatin-protein adaptor activity / poly(A)+ mRNA export from nucleus / transcription repressor complex / negative regulation of innate immune response / transcription corepressor activity / protein transport / nuclear envelope / defense response to Gram-negative bacterium / single-stranded RNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear transport factor 2/Mtr2 / 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 (NTF2) domain ...Nuclear transport factor 2/Mtr2 / 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 (NTF2) domain / Nuclear transport factor 2 domain / Nuclear Transport Factor 2; Chain: A, - #50 / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NTF2-related export protein / Nuclear RNA export factor 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: 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
DepositionOct 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Nuclear RNA export factor 2
U: NTF2-related export protein
B: Nuclear RNA export factor 2
V: NTF2-related export protein


Theoretical massNumber of molelcules
Total (without water)77,6834
Polymers77,6834
Non-polymers00
Water30617
1
A: Nuclear RNA export factor 2
U: NTF2-related export protein


Theoretical massNumber of molelcules
Total (without water)38,8422
Polymers38,8422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-13 kcal/mol
Surface area15190 Å2
MethodPISA
2
B: Nuclear RNA export factor 2
V: NTF2-related export protein


Theoretical massNumber of molelcules
Total (without water)38,8422
Polymers38,8422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-12 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.540, 74.090, 155.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear RNA export factor 2


Mass: 23645.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nxf2, CG4118 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9VV73
#2: Protein NTF2-related export protein / p15


Mass: 15195.997 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Nxt1, CG12752 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9V3H8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.6 M magnesium sulfate

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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: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→77.9 Å / Num. obs: 19083 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.412 / Num. unique obs: 2732 / CC1/2: 0.904 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JKG

1jkg


Resolution: 2.8→66.91 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.672 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26259 1904 10 %RANDOM
Rwork0.21207 ---
obs0.21705 17130 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.085 Å2
Baniso -1Baniso -2Baniso -3
1-4.45 Å20 Å2-0 Å2
2---2.68 Å20 Å2
3----1.77 Å2
Refinement stepCycle: 1 / Resolution: 2.8→66.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5101 0 0 17 5118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135195
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174721
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6447008
X-RAY DIFFRACTIONr_angle_other_deg1.2851.57910915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3865619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26721.938325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.56615899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5251544
X-RAY DIFFRACTIONr_chiral_restr0.0650.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8624.1582506
X-RAY DIFFRACTIONr_mcbond_other2.8624.1572505
X-RAY DIFFRACTIONr_mcangle_it4.636.2253115
X-RAY DIFFRACTIONr_mcangle_other4.6296.2263116
X-RAY DIFFRACTIONr_scbond_it3.0524.5332689
X-RAY DIFFRACTIONr_scbond_other3.0534.5312687
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9526.663893
X-RAY DIFFRACTIONr_long_range_B_refined7.42647.595578
X-RAY DIFFRACTIONr_long_range_B_other7.42547.5995579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 137 -
Rwork0.259 1233 -
obs--99.85 %

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