[English] 日本語
Yorodumi- PDB-3fmp: Crystal structure of the nucleoporin Nup214 in complex with the D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fmp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19 | ||||||
Components |
| ||||||
Keywords | Oncoprotein/Hydrolase / nuclear porin / nuclear pore complex / nucleocytoplasmic transport / mRNA export / protein interaction / helicase / beta-propeller / DEAD box / Glycoprotein / mRNA transport / Nucleus / Phosphoprotein / Protein transport / Proto-oncogene / Translocation / Transport / ATP-binding / Hydrolase / Membrane / Nucleotide-binding / RNA-binding / Protein transport-Hydrolase COMPLEX / Oncoprotein-Hydrolase COMPLEX | ||||||
Function / homology | Function and homology information cytoplasmic side of nuclear pore / HuR (ELAVL1) binds and stabilizes mRNA / regulation of nucleocytoplasmic transport / nuclear export signal receptor activity / 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 ...cytoplasmic side of nuclear pore / HuR (ELAVL1) binds and stabilizes mRNA / regulation of nucleocytoplasmic transport / nuclear export signal receptor activity / 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 / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / 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 / RNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / 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 / SUMOylation of DNA damage response and repair proteins / nuclear pore / protein export from nucleus / SUMOylation of chromatin organization proteins / helicase activity / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / cytoplasmic stress granule / HCMV Early Events / protein import into nucleus / nuclear envelope / snRNP Assembly / RNA helicase activity / regulation of cell cycle / RNA helicase / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å | ||||||
Authors | Napetschnig, J. / Debler, E.W. / Blobel, G. / Hoelz, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19. Authors: Napetschnig, J. / Kassube, S.A. / Debler, E.W. / Wong, R.W. / Blobel, G. / Hoelz, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fmp.cif.gz | 262.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fmp.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fmp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3fmp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3fmp_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 3fmp_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fmp ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fmp | HTTPS FTP |
-Related structure data
Related structure data | 3fmoSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | chains A,B / chains C,D |
-Components
#1: Protein | Mass: 49730.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUP214, CAIN, CAN, KIAA0023 / Production host: Escherichia coli (E. coli) / References: UniProt: P35658 #2: Protein | Mass: 53994.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX19B, DBP5, DDX19 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UMR2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.34 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 3000, CHES buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2008 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 32548 / Num. obs: 29717 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.113 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3249 / Rsym value: 0.395 / % possible all: 70.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FMO Resolution: 3.19→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 45.736 / SU ML: 0.369 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.572 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.611 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.19→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.269 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|