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- PDB-3hxr: Nucleoporin Nup120 from S.cerevisiae (aa 1-757) -

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Basic information

Entry
Database: PDB / ID: 3hxr
TitleNucleoporin Nup120 from S.cerevisiae (aa 1-757)
ComponentsNucleoporin NUP120
KeywordsSTRUCTURAL PROTEIN / Coiled coil / Membrane / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / nuclear pore outer ring / telomere tethering at nuclear periphery / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore ...mRNA export from nucleus in response to heat stress / nuclear pore localization / nuclear pore outer ring / telomere tethering at nuclear periphery / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / mRNA export from nucleus / nuclear pore / protein export from nucleus / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
Nucleoporin Nup120/160 / Nucleoporin Nup120/160
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLeksa, N.C. / Brohawn, S.G. / Schwartz, T.U.
CitationJournal: Structure / Year: 2009
Title: The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture.
Authors: Leksa, N.C. / Brohawn, S.G. / Schwartz, T.U.
History
DepositionJun 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin NUP120


Theoretical massNumber of molelcules
Total (without water)88,0661
Polymers88,0661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.600, 153.690, 52.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 88065.828 Da / Num. of mol.: 1 / Fragment: UNP residues 1-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP120, RAT2, YKL057C, YKL314, YKL313 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P35729

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.2M KSCN, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19288 / % possible obs: 99.8 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 3 % / Biso Wilson estimate: 82.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 20.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 3 % / Rsym value: 0.59 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→48.09 Å / SU ML: 0.99 / σ(F): 1.9 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.299 1834 5.12 %
Rwork0.244 --
obs0.247 19288 99.6 %
all-35978 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.24 Å2 / ksol: 0.31 e/Å3
Refinement stepCycle: LAST / Resolution: 3→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 0 0 5313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.017
X-RAY DIFFRACTIONf_angle_d1.915
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08660.34351170.30252534X-RAY DIFFRACTION97
3.0866-3.17740.33721270.3032628X-RAY DIFFRACTION100
3.1774-3.280.27891280.28112649X-RAY DIFFRACTION100
3.28-3.39720.28751710.27452606X-RAY DIFFRACTION100
3.3972-3.53320.27621570.25212615X-RAY DIFFRACTION100
3.5332-3.69390.31881410.24752626X-RAY DIFFRACTION100
3.6939-3.88860.32831570.2392593X-RAY DIFFRACTION100
3.8886-4.13210.29381530.22152622X-RAY DIFFRACTION100
4.1321-4.45090.2941140.20762671X-RAY DIFFRACTION100
4.4509-4.89840.22881030.19272655X-RAY DIFFRACTION100
4.8984-5.60630.26731730.20722585X-RAY DIFFRACTION100
5.6063-7.05980.32541580.26882611X-RAY DIFFRACTION100
7.0598-48.09580.28271350.23732612X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4663-0.00222.25044.69210.78763.9761-0.1666-0.60031.2980.3150.1346-0.8494-0.25210.47130.0020.1154-0.120.10540.2773-0.24610.6297119.066738.746827.5949
20.1677-0.09140.33050.462-0.08890.6708-1.064-0.09290.92580.8064-1.0157-0.1579-1.66310.2055-0.01580.75910.01440.05490.4676-0.32421.8565112.055256.371529.1313
33.59290.53390.70813.34060.55152.86490.0114-0.34861.4379-0.0764-0.09810.49-0.327-0.41860.004-0.12880.00910.17150.1459-0.17410.248998.967837.106224.2158
45.14951.00110.84355.21530.60732.13410.15880.5858-0.1971-0.56640.00770.24250.4769-0.0011-0.01370.30740.0463-0.11920.25220.1103-0.19196.78927.55266.3297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 0:163)A0 - 163
2X-RAY DIFFRACTION2CHAIN A AND RESID 164:181)A164 - 181
3X-RAY DIFFRACTION3CHAIN A AND RESID 182:503)A182 - 503
4X-RAY DIFFRACTION4CHAIN A AND RESID 504:730)A504 - 730

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