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- PDB-6iew: The crystal structure of the dNxf2 UBA domain in complex with Pan... -

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Basic information

Entry
Database: PDB / ID: 6iew
TitleThe crystal structure of the dNxf2 UBA domain in complex with Panoramix
ComponentsFusion protein of Nuclear RNA export factor 2 and Protein panoramix
KeywordsPROTEIN BINDING / piRNA
Function / homology
Function and homology information


Transport of Mature mRNA derived from an Intron-Containing Transcript / piRNA-mediated heterochromatin formation / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / poly(A)+ mRNA export from nucleus / transcription repressor complex / single-stranded RNA binding / negative regulation of gene expression / RNA binding ...Transport of Mature mRNA derived from an Intron-Containing Transcript / piRNA-mediated heterochromatin formation / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / poly(A)+ mRNA export from nucleus / transcription repressor complex / single-stranded RNA binding / negative regulation of gene expression / 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 transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. ...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 transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / 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 / SAD / Resolution: 1.5 Å
AuthorsHuang, Y. / Cheng, S.
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 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Fusion protein of Nuclear RNA export factor 2 and Protein panoramix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3412
Polymers10,2491
Non-polymers921
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, In the previous gel filtration experiments, dNxf2-UBA co-migrated with Panx at a 1:1 ratio. In the construct for crystallization, we connected dNxf2-UBA (chain A) and Panx ...Evidence: gel filtration, In the previous gel filtration experiments, dNxf2-UBA co-migrated with Panx at a 1:1 ratio. In the construct for crystallization, we connected dNxf2-UBA (chain A) and Panx (chain B) using (Gly-Ser) linker.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.074, 40.925, 83.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Fusion protein of Nuclear RNA export factor 2 and Protein panoramix / Protein silencio


Mass: 10248.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nxf2, CG4118, Panx, CG9754 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VV73, UniProt: Q9W2H9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 30%(w/v) PEG3350, 0.1M Tris (pH 9.0), 0.2M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 16378 / % possible obs: 98.8 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 21.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1469 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data collection
Cootmodel building
PHENIXphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.074 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 15.52
RfactorNum. reflection% reflection
Rfree0.1732 1638 10 %
Rwork0.1637 --
obs0.1647 16378 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 0 216 930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003748
X-RAY DIFFRACTIONf_angle_d0.641011
X-RAY DIFFRACTIONf_dihedral_angle_d13.001284
X-RAY DIFFRACTIONf_chiral_restr0.056116
X-RAY DIFFRACTIONf_plane_restr0.003129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4997-1.54390.21231220.1861101X-RAY DIFFRACTION89
1.5439-1.59370.19911290.17271165X-RAY DIFFRACTION97
1.5937-1.65060.1891360.15831220X-RAY DIFFRACTION100
1.6506-1.71670.17181370.15621234X-RAY DIFFRACTION100
1.7167-1.79480.17051360.16311221X-RAY DIFFRACTION100
1.7948-1.88940.20321350.16691213X-RAY DIFFRACTION100
1.8894-2.00780.20041370.16791232X-RAY DIFFRACTION100
2.0078-2.16280.16211370.14821235X-RAY DIFFRACTION100
2.1628-2.38030.1711380.15361245X-RAY DIFFRACTION100
2.3803-2.72460.15641390.1711251X-RAY DIFFRACTION100
2.7246-3.43180.16741420.16491273X-RAY DIFFRACTION100
3.4318-29.07950.16711500.16591350X-RAY DIFFRACTION100

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