+Open data
-Basic information
Entry | Database: PDB / ID: 1n54 | ||||||
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Title | Cap Binding Complex m7GpppG free | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / CBP80 / CBBP20 / Nuclear cap binding complex / m7GpppG / RNP domain | ||||||
Function / homology | Function and homology information snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding ...snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / positive regulation of RNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated post-transcriptional gene silencing / : / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / regulation of translational initiation / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / spliceosomal complex assembly / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / 7-methylguanosine mRNA capping / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Formation of HIV-1 elongation complex containing HIV-1 Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / snRNP Assembly / positive regulation of cell growth / defense response to virus / molecular adaptor activity / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Calero, G. / Wilson, K. / Ly, T. / Rios-Steiner, J. / Clardy, J. / Cerione, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural basis of m7GpppG binding to the nuclear cap-binding protein complex. Authors: Calero, G. / Wilson, K. / Ly, T. / Rios-Steiner, J. / Clardy, J. / Cerione, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n54.cif.gz | 193.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n54.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n54 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n54 | HTTPS FTP |
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-Related structure data
Related structure data | 1n52SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 91960.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBP80 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09161 | ||
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#2: Protein | Mass: 18028.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBP20 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P52298 | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.03 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: Peg 400, Magnesium chloride, glycerol, Tris, glycine, ethylene glycol, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.943 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.943 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.49 Å / Num. all: 39454 / Num. obs: 33886 / Observed criterion σ(I): 3 / Redundancy: 11 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.079 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.69→2.85 Å / Mean I/σ(I) obs: 2.3 |
Reflection | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 40 Å / Num. obs: 39454 / % possible obs: 100 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1N52 Resolution: 2.72→24.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 3238611.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber Details: Data set had 15% twinning. Used CNS twinning refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.25 Å2 / ksol: 0.26 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.72→24.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.84 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.245 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.43 / Rfactor Rwork: 0.39 |