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- PDB-3i5p: Nup170(aa979-1502), S.cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3i5p
TitleNup170(aa979-1502), S.cerevisiae
ComponentsNucleoporin NUP170
KeywordsPROTEIN TRANSPORT / HELICAL STACK / Membrane / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Translocation / Transmembrane / Transport
Function / homology
Function and homology information


nuclear pore inner ring / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore complex assembly / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / mRNA transport / heterochromatin formation ...nuclear pore inner ring / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore complex assembly / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / mRNA transport / heterochromatin formation / nuclear pore / chromosome segregation / promoter-specific chromatin binding / protein import into nucleus / nuclear envelope / nuclear membrane / chromatin binding / protein-containing complex binding
Similarity search - Function
Nucleoporin, helical C-terminal domain / Nucleoporin, helical domain, N-terminal subdomain / Nucleoporin, helical domain, central subdomain / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like ...Nucleoporin, helical C-terminal domain / Nucleoporin, helical domain, N-terminal subdomain / Nucleoporin, helical domain, central subdomain / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsWhittle, J.R.R. / Schwartz, T.U.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element.
Authors: Whittle, J.R. / Schwartz, T.U.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)61,1211
Polymers61,1211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.370, 121.370, 256.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 61120.598 Da / Num. of mol.: 1 / Fragment: HELICAL DOMAIN (UNP residues 980-1502)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NLE3, NUP170, YBL0725, YBL079W / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P38181

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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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, 8% PEG 3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 12125 / Num. obs: 12125 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.31 Å / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→28.966 Å / SU ML: 0.96 / σ(F): 1.34 / Phase error: 43.59 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3241 444 3.72 %RANDOM
Rwork0.3067 ---
all0.3074 11936 --
obs0.3074 11936 96.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 114.564 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.5842 Å2-0 Å2-0 Å2
2--23.5842 Å2-0 Å2
3----47.1683 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 0 0 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043625
X-RAY DIFFRACTIONf_angle_d0.734900
X-RAY DIFFRACTIONf_dihedral_angle_d14.2211260
X-RAY DIFFRACTIONf_chiral_restr0.047549
X-RAY DIFFRACTIONf_plane_restr0.002619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2003-3.66260.47071380.37223548X-RAY DIFFRACTION91
3.6626-4.61150.37111490.3113915X-RAY DIFFRACTION100
4.6115-28.96720.27461570.29024029X-RAY DIFFRACTION100

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