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- PDB-4ifq: Crystal structure of Saccharomyces cerevisiae NUP192, residues 2 ... -

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Basic information

Entry
Database: PDB / ID: 4ifq
TitleCrystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)]
ComponentsNucleoporin NUP192
KeywordsPROTEIN TRANSPORT / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium / alpha solenoid-like / Nuclear Pore Complex component / NPC / Nup192 / Nup188 / Nucleoporin / Nucleocytoplasmic Transport: a Target for Cellular Control / NPCXstals
Function / homology
Function and homology information


nuclear pore inner ring / regulation of nucleocytoplasmic transport / nuclear pore organization / 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 / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport ...nuclear pore inner ring / regulation of nucleocytoplasmic transport / nuclear pore organization / 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 / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / mRNA transport / nuclear pore / protein transport / nuclear envelope / nucleus
Similarity search - Function
Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205
Similarity search - Domain/homology
IODIDE ION / Nucleoporin NUP192
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)
CitationJournal: Structure / Year: 2013
Title: Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.
Authors: Parthasarathy Sampathkumar / Seung Joong Kim / Paula Upla / William J Rice / Jeremy Phillips / Benjamin L Timney / Ursula Pieper / Jeffrey B Bonanno / Javier Fernandez-Martinez / Zhanna ...Authors: Parthasarathy Sampathkumar / Seung Joong Kim / Paula Upla / William J Rice / Jeremy Phillips / Benjamin L Timney / Ursula Pieper / Jeffrey B Bonanno / Javier Fernandez-Martinez / Zhanna Hakhverdyan / Natalia E Ketaren / Tsutomu Matsui / Thomas M Weiss / David L Stokes / J Michael Sauder / Stephen K Burley / Andrej Sali / Michael P Rout / Steven C Almo /
Abstract: The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure ...The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC's inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2-960 [ScNup192(2-960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2-960) could undergo long-range transition between "open" and "closed" conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2-960), and homology modeling. Evolutionary analyses using the ScNup192(2-960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Structure summary
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3May 22, 2013Group: Database references
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations
Category: citation_author / struct_conn ...citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: 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: Nucleoporin NUP192
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,34015
Polymers111,7791
Non-polymers1,56114
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoporin NUP192
hetero molecules

A: Nucleoporin NUP192
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,68030
Polymers223,5592
Non-polymers3,12228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6100 Å2
ΔGint-177 kcal/mol
Surface area71940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.600, 134.600, 234.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsTHE DIMERIC INTERFACE SUGGESTED BY PISA IS LIKELY TO BE NON-BIOLOGICAL

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Components

#1: Protein Nucleoporin NUP192 / Nuclear pore protein NUP192


Mass: 111779.430 Da / Num. of mol.: 1 / Fragment: UNP residues 2-960
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: J1216, NUP192, YJL039C / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: P47054
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.76 Å3/Da / Density % sol: 74.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor ...Details: Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2012 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.254→50 Å / Num. all: 64698 / Num. obs: 64698 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 78 Å2 / Rsym value: 0.136 / Net I/σ(I): 17.5
Reflection shellResolution: 3.25→3.29 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2186 / Rsym value: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: Built using AutoBuild (Phenix) and Buccaneer (CCP4)

Resolution: 3.25→47.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 15.519 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.753 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1930 5.6 %RANDOM
Rwork0.1875 ---
obs0.1905 34573 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 184.54 Å2 / Biso mean: 85.2254 Å2 / Biso min: 41.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2--2.15 Å20 Å2
3----4.29 Å2
Refinement stepCycle: LAST / Resolution: 3.25→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6923 0 42 6 6971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197103
X-RAY DIFFRACTIONr_bond_other_d0.0050.026692
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9659620
X-RAY DIFFRACTIONr_angle_other_deg0.885315383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2285847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47824.726347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.906151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881527
X-RAY DIFFRACTIONr_chiral_restr0.0850.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021694
LS refinement shellResolution: 3.254→3.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 148 -
Rwork0.265 2331 -
all-2479 -
obs--98.88 %

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