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- PDB-2osz: Structure of Nup58/45 suggests flexible nuclear pore diameter by ... -

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Basic information

Entry
Database: PDB / ID: 2osz
TitleStructure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding
ComponentsNucleoporin p58/p45
KeywordsSTRUCTURAL PROTEIN / NPC / nucleoporin
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins ...Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / regulation of protein import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear localization sequence binding / structural constituent of nuclear pore / nucleocytoplasmic transport / mRNA transport / nuclear pore / nuclear envelope / protein transport / nuclear membrane / protein-containing complex binding / protein-containing complex / identical protein binding
Similarity search - Function
Helix Hairpins - #1350 / Nucleoporin FG repeated region / Nucleoporin p58/p45 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsMelcak, I. / Hoelz, A. / Blobel, G.
CitationJournal: Science / Year: 2007
Title: Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding.
Authors: Melcak, I. / Hoelz, A. / Blobel, G.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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 p58/p45
B: Nucleoporin p58/p45
C: Nucleoporin p58/p45
D: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)43,1254
Polymers43,1254
Non-polymers00
Water1,42379
1
A: Nucleoporin p58/p45
B: Nucleoporin p58/p45

A: Nucleoporin p58/p45
B: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)43,1254
Polymers43,1254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
2
C: Nucleoporin p58/p45
D: Nucleoporin p58/p45

C: Nucleoporin p58/p45
D: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)43,1254
Polymers43,1254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.705, 92.705, 169.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

21A-59-

HOH

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Components

#1: Protein
Nucleoporin p58/p45 / Nucleoporin-like 1


Mass: 10781.189 Da / Num. of mol.: 4 / Fragment: residues 327-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nupl1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P70581
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 4.49 Å3/Da / Density % sol: 72.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 100 mM Bis-Tris, 600 mM CaCl2, 2.7% (w/v) Benzamidine-HCl, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00813
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00813 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 17216 / % possible obs: 95.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.098 / Χ2: 1.005 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.954.20.38917131.007198.1
2.95-3.074.30.33417381.008198.1
3.07-3.214.30.25517061.005197.3
3.21-3.384.30.18917181.007197.4
3.38-3.594.30.11317261.005197
3.59-3.864.30.08817321.004196.9
3.86-4.254.30.0717071.006196
4.25-4.854.30.06617241.004195
4.85-6.094.20.07517091.006193
6.09-204.10.04717431189

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.85→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflectionSelection details
Rfree0.288 1611 random
Rwork0.25 --
all-17894 -
obs-16208 -
Displacement parametersBiso mean: 41.299 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 0 79 2931

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