+Open data
-Basic information
Entry | Database: PDB / ID: 1n52 | ||||||
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Title | Cap Binding Complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / CBP80 / CBP20 / RNP domain / cap binding protein / m7GpppG | ||||||
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: 2.11 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 | 1n52.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n52.ent.gz | 159.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n52 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n52 | HTTPS FTP |
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-Related structure data
Related structure data | 1n54C 1h6kS 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
-Protein , 2 types, 2 molecules AB
#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 |
-Non-polymers , 5 types, 357 molecules
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | ChemComp-PG4 / | ||||
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-GTG / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: PEG 400, magnesium chloride, 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 |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.12→37.45 Å / Num. all: 135299 / Num. obs: 132887 / % possible obs: 98 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 6 % / Biso Wilson estimate: 14.9 Å2 / Limit h max: 48 / Limit h min: -27 / Limit k max: 55 / Limit k min: -27 / Limit l max: 88 / Limit l min: -88 / Observed criterion F max: 3903632.29 / Observed criterion F min: 0.2 / Rmerge(I) obs: 0.33 / Rsym value: 0.067 / Net I/σ(I): 16 | |||||||||||||||
Reflection shell | Resolution: 2.11→2.17 Å / Mean I/σ(I) obs: 2.4 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 78602 / % possible obs: 99 % / Rmerge(I) obs: 0.058 | |||||||||||||||
Reflection shell | *PLUS Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1H6K Resolution: 2.11→24.54 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1.07 / Occupancy min: 1 / Data cutoff high absF: 3917587.28 / Data cutoff high rms absF: 3917587.28 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 45.8457 Å2 / ksol: 0.343953 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.13 Å2 / Biso mean: 49.2 Å2 / Biso min: 15.89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.11→24.54 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.12 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.2427 / Rfactor Rwork: 0.2256 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.37 / Rfactor Rwork: 0.32 |