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- PDB-2qx5: Structure of nucleoporin Nic96 -

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Basic information

Entry
Database: PDB / ID: 2qx5
TitleStructure of nucleoporin Nic96
ComponentsNucleoporin NIC96
KeywordsTRANSPORT PROTEIN / nucleoporin / mRNA transport / Nuclear pore complex / Nucleus / Protein transport / Translocation / Transport
Function / homology
Function and homology information


nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport ...nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / protein import into nucleus / nuclear envelope / nuclear membrane
Similarity search - Function
Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJeudy, S. / Schwartz, T.U.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture
Authors: Jeudy, S. / Schwartz, T.U.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin NIC96
B: Nucleoporin NIC96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8304
Polymers151,7592
Non-polymers712
Water2,216123
1
A: Nucleoporin NIC96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9152
Polymers75,8791
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NIC96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9152
Polymers75,8791
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.121, 82.478, 113.028
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoporin NIC96 / Nuclear pore protein NIC96 / 96 kDa nucleoporin- interacting component


Mass: 75879.398 Da / Num. of mol.: 2 / Fragment: residues 186-839
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: NIC96 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P34077
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 18% PEG 3350, 0.1M Bis Tris propane, 0.2M Potassium Thiocyanate, 1mM Cetyltrimethylammonium bromide, pH 8.2, 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: 1.0718 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 55385 / Num. obs: 55097 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 47.7 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.381 / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2756 -RANDOM
Rwork0.233 ---
obs-54858 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9035 0 2 123 9160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.712
X-RAY DIFFRACTIONf_bond_d0.005
LS refinement shellResolution: 2.5→2.54 Å
RfactorNum. reflection% reflection
Rfree0.318 138 -
Rwork0.286 --
obs-2502 98.8 %

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