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- PDB-6ihj: Crystal structure of Drosophila Nxf1 NTF2 domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6ihj
TitleCrystal structure of Drosophila Nxf1 NTF2 domain in complex with Nxt1/p15
Components
  • NTF2-related export protein
  • Nuclear RNA export factor 1
KeywordsPROTEIN TRANSPORT / Nuclear Export Factor / Drosophila / Nxf2 / NTF2 domain / p15 / Nxt1
Function / homology
Function and homology information


Transport of Mature mRNA derived from an Intron-Containing Transcript / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of RNA export from nucleus / nuclear pore central transport channel / nuclear export / poly(A)+ mRNA export from nucleus / ribonucleoprotein complex binding / mRNA export from nucleus ...Transport of Mature mRNA derived from an Intron-Containing Transcript / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of RNA export from nucleus / nuclear pore central transport channel / nuclear export / poly(A)+ mRNA export from nucleus / ribonucleoprotein complex binding / mRNA export from nucleus / transcription repressor complex / negative regulation of innate immune response / nuclear envelope / protein transport / nuclear membrane / defense response to Gram-negative bacterium / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / 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 RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / 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 / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat profile. / Leucine-rich repeat / RNA-binding domain superfamily / Leucine-rich repeat domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Nuclear RNA export factor 1 / NTF2-related export protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuang, Y. / Yuan, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China91640102 China
National Natural Science Foundation of China31870741 China
CitationJournal: Nat.Cell Biol. / Year: 2019
Title: A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation.
Authors: Zhao, K. / Cheng, S. / Miao, N. / Xu, P. / Lu, X. / Zhang, Y. / Wang, M. / Ouyang, X. / Yuan, X. / Liu, W. / Lu, X. / Zhou, P. / Gu, J. / Zhang, Y. / Qiu, D. / Jin, Z. / Su, C. / Peng, C. / ...Authors: Zhao, K. / Cheng, S. / Miao, N. / Xu, P. / Lu, X. / Zhang, Y. / Wang, M. / Ouyang, X. / Yuan, X. / Liu, W. / Lu, X. / Zhou, P. / Gu, J. / Zhang, Y. / Qiu, D. / Jin, Z. / Su, C. / Peng, C. / Wang, J.H. / Dong, M.Q. / Wan, Y. / Ma, J. / Cheng, H. / Huang, Y. / Yu, Y.
History
DepositionSep 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 1
C: Nuclear RNA export factor 1
B: NTF2-related export protein
D: NTF2-related export protein


Theoretical massNumber of molelcules
Total (without water)74,9744
Polymers74,9744
Non-polymers00
Water25214
1
A: Nuclear RNA export factor 1
B: NTF2-related export protein


Theoretical massNumber of molelcules
Total (without water)37,4872
Polymers37,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-24 kcal/mol
Surface area13060 Å2
MethodPISA
2
C: Nuclear RNA export factor 1
D: NTF2-related export protein


Theoretical massNumber of molelcules
Total (without water)37,4872
Polymers37,4872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.204, 152.204, 49.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Nuclear RNA export factor 1 / Protein small bristles / DmNXF1 / Protein tip-associating


Mass: 22147.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sbr, nxf1, CG1664 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U1H9
#2: Protein NTF2-related export protein / p15 / Nxt1


Mass: 15340.127 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) / References: UniProt: Q9V3H8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 16%(w/v) PEG 8000, 40mM Potassium phosphate dibasic and 20%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 18389 / % possible obs: 99.8 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 22.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 1822 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JKG

1jkg


Resolution: 2.7→28.764 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2692 1830 9.95 %
Rwork0.2239 --
obs0.2284 18389 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 0 14 4377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044439
X-RAY DIFFRACTIONf_angle_d0.7146041
X-RAY DIFFRACTIONf_dihedral_angle_d5.0652606
X-RAY DIFFRACTIONf_chiral_restr0.046710
X-RAY DIFFRACTIONf_plane_restr0.004777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.32531440.25951289X-RAY DIFFRACTION100
2.773-2.85450.30971350.2491238X-RAY DIFFRACTION100
2.8545-2.94650.30391430.25011272X-RAY DIFFRACTION100
2.9465-3.05170.31651380.24121257X-RAY DIFFRACTION100
3.0517-3.17380.2481460.22811262X-RAY DIFFRACTION100
3.1738-3.3180.30091430.22131280X-RAY DIFFRACTION100
3.318-3.49270.23911390.21921247X-RAY DIFFRACTION100
3.4927-3.71110.25421410.20931272X-RAY DIFFRACTION100
3.7111-3.99690.25511400.22051274X-RAY DIFFRACTION100
3.9969-4.39790.27671390.21091281X-RAY DIFFRACTION100
4.3979-5.03130.24611400.18541290X-RAY DIFFRACTION100
5.0313-6.32780.29151430.25171301X-RAY DIFFRACTION100
6.3278-28.76550.25641390.23691296X-RAY DIFFRACTION97

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