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- PDB-3cqc: Nucleoporin Nup107/Nup133 interaction complex -

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Basic information

Entry
Database: PDB / ID: 3cqc
TitleNucleoporin Nup107/Nup133 interaction complex
Components
  • Nuclear pore complex protein Nup107
  • Nuclear pore complex protein Nup133
KeywordsPROTEIN TRANSPORT / Nucleoporin / Nuclear Pore Complex / mRNA transport / Nucleus / Phosphoprotein / Translocation
Function / homology
Function and homology information


nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / somite development / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus ...nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / somite development / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / neural tube development / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / female gonad development / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA export from nucleus / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / neurogenesis / nuclear periphery / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / kinetochore / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1380 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #700 / Delta-Endotoxin; domain 1 - #50 / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Delta-Endotoxin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1380 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #700 / Delta-Endotoxin; domain 1 - #50 / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Delta-Endotoxin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup133
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å
AuthorsJeudy, S. / Boehmer, T. / Berke, I. / Schwartz, T.U.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex.
Authors: Boehmer, T. / Jeudy, S. / Berke, I.C. / Schwartz, T.U.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nuclear pore complex protein Nup107
B: Nuclear pore complex protein Nup133


Theoretical massNumber of molelcules
Total (without water)57,4952
Polymers57,4952
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-17.6 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.744, 127.936, 152.738
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nuclear pore complex protein Nup107 / Nucleoporin Nup107 / 107 kDa nucleoporin


Mass: 31319.990 Da / Num. of mol.: 1 / Fragment: residues 658-925
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP107 / Plasmid: pGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P57740
#2: Protein Nuclear pore complex protein Nup133 / Nucleoporin Nup133 / 133 kDa nucleoporin


Mass: 26174.842 Da / Num. of mol.: 1 / Fragment: residues 935-1156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP133 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8WUM0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4.36 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes, 1.1M sodium malonate, 1-1.5% PEG MME 5000, pH 7.0, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2006 / 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: 2.53→40 Å / Num. all: 32441 / Num. obs: 32244 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 49.1 Å2 / Rsym value: 0.105 / Net I/σ(I): 16.1
Reflection shellResolution: 2.53→2.64 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.487 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.53→39.633 Å / SU ML: 0.32 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1629 5.06 %
Rwork0.2169 --
obs0.2184 32203 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.208 Å2 / ksol: 0.325 e/Å3
Refinement stepCycle: LAST / Resolution: 2.53→39.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 0 136 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093416
X-RAY DIFFRACTIONf_angle_d1.0964608
X-RAY DIFFRACTIONf_dihedral_angle_d16.3161259
X-RAY DIFFRACTIONf_chiral_restr0.072525
X-RAY DIFFRACTIONf_plane_restr0.004584
LS refinement shellResolution: 2.53→2.61 Å
RfactorNum. reflection% reflection
Rfree0.286 122 -
Rwork0.264 --
obs--87 %

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