[English] 日本語
Yorodumi- PDB-3cqg: Nucleoporin Nup107/Nup133 interaction complex, delta finger mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cqg | ||||||
---|---|---|---|---|---|---|---|
Title | Nucleoporin Nup107/Nup133 interaction complex, delta finger mutant | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / Nucleoporins / 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 / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / 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 / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / neural tube development / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / neurogenesis / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / kinetochore / ISG15 antiviral mechanism / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Jeudy, S. / Boehmer, T. / Berke, I. / Schwartz, T.U. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3cqg.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3cqg.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/3cqg ftp://data.pdbj.org/pub/pdb/validation_reports/cq/3cqg | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28192.301 Da / Num. of mol.: 1 Fragment: residues 658-771, 802-925, connected by linker GGSGGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUP107 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P57740 |
---|---|
#2: Protein | Mass: 26181.793 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: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8WUM0 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 25-27% PEG 2000 MME, 500mM KSCN, 0.1M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 12890 / Num. obs: 12599 / % possible obs: 97.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 74.9 Å2 / Rsym value: 0.098 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1195 / Rsym value: 0.524 / % possible all: 97.3 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 3→46 Å / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→46 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 3→3.14 Å
|