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- PDB-3i5q: Nup170(aa1253-1502) at 2.2 A, S.cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3i5q
TitleNup170(aa1253-1502) at 2.2 A, 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 / chromosome, subtelomeric region / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / telomere tethering at nuclear periphery / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins ...nuclear pore inner ring / protein localization to nuclear inner membrane / chromosome, subtelomeric region / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / telomere tethering at nuclear periphery / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / mRNA transport / nuclear pore / chromosome segregation / promoter-specific chromatin binding / heterochromatin formation / protein import into nucleus / nuclear envelope / nuclear membrane / chromatin binding / protein-containing complex binding
Similarity search - Function
Regulator of G-protein Signalling 4; domain 2 - #20 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1050 / 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 / Regulator of G-protein Signalling 4; domain 2 ...Regulator of G-protein Signalling 4; domain 2 - #20 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1050 / 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 / Regulator of G-protein Signalling 4; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 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 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
B: Nucleoporin NUP170
A: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)58,5592
Polymers58,5592
Non-polymers00
Water6,846380
1
B: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)29,2791
Polymers29,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)29,2791
Polymers29,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Nucleoporin NUP170
A: Nucleoporin NUP170

B: Nucleoporin NUP170
A: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)117,1184
Polymers117,1184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9690 Å2
ΔGint-23 kcal/mol
Surface area44680 Å2
MethodPISA
4
A: Nucleoporin NUP170

B: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)58,5592
Polymers58,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.432, 113.005, 150.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 29279.494 Da / Num. of mol.: 2 / Fragment: C-terminal fragment (UNP residues 1253-1502)
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 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: 2.2→30 Å / Num. all: 33936 / Num. obs: 33936 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→30.15 Å / SU ML: 1.88 / σ(F): 0.09 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 1665 5.12 %RANDOM
Rwork0.2316 ---
all0.2337 32535 --
obs0.2337 32535 95.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.38 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.3386 Å2-0 Å20 Å2
2---1.2127 Å20 Å2
3---7.5513 Å2
Refinement stepCycle: LAST / Resolution: 2.204→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 0 380 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064142
X-RAY DIFFRACTIONf_angle_d0.8545590
X-RAY DIFFRACTIONf_dihedral_angle_d17.1221496
X-RAY DIFFRACTIONf_chiral_restr0.057624
X-RAY DIFFRACTIONf_plane_restr0.003706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2043-2.26910.32481140.27282187X-RAY DIFFRACTION81
2.2691-2.34230.31621220.26142395X-RAY DIFFRACTION91
2.3423-2.4260.32031280.24892501X-RAY DIFFRACTION93
2.426-2.52310.30321400.23872483X-RAY DIFFRACTION93
2.5231-2.63780.27011420.23742503X-RAY DIFFRACTION94
2.6378-2.77680.27641590.24022561X-RAY DIFFRACTION96
2.7768-2.95070.27671290.25882636X-RAY DIFFRACTION98
2.9507-3.17830.26641530.24892656X-RAY DIFFRACTION98
3.1783-3.49770.31161320.23632695X-RAY DIFFRACTION99
3.4977-4.00280.25341610.21382677X-RAY DIFFRACTION99
4.0028-5.03930.24561460.20462733X-RAY DIFFRACTION99
5.0393-30.15270.2321390.21662843X-RAY DIFFRACTION99

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