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Yorodumi- PDB-1h2u: Structure of the human nuclear cap-binding-complex (CBC) in compl... -
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-Basic information
Entry | Database: PDB / ID: 1h2u | ||||||
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Title | Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / M7GCAP / CAP-BINDING-COMPLEX / RNP DOMAIN / MIF4G DOMAIN / RNA MATURATION / RNA EXPORT / RNA-BINDING | ||||||
Function / homology | Function and homology information positive regulation of RNA 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 ...positive regulation of RNA 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 / RNA cap binding / alternative mRNA splicing, via spliceosome / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / mRNA 3'-end processing / RNA catabolic process / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of mRNA splicing, via spliceosome / regulation of translational initiation / FGFR2 alternative splicing / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / positive regulation of transcription elongation by RNA polymerase II / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / mRNA transcription by RNA polymerase II / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / positive regulation of cell growth / snRNP Assembly / defense response to virus / molecular adaptor activity / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Mazza, C. / Segref, A. / Mattaj, I.W. / Cusack, S. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Large-Scale Induced Fit Recognition of an M(7)Gpppg CAP Analogue by the Human Nuclear CAP-Binding Complex Authors: Mazza, C. / Segref, A. / Mattaj, I.W. / Cusack, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Co-Crystallization of the Human Nuclear CAP-Binding Complex with a M7Gpppg CAP Analogue Using Protein Engineering Authors: Mazza, C. / Segref, A. / Mattaj, I. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h2u.cif.gz | 384.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h2u.ent.gz | 310.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h2u_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1h2u_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1h2u_validation.xml.gz | 74.9 KB | Display | |
Data in CIF | 1h2u_validation.cif.gz | 109.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h2u ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h2u | HTTPS FTP |
-Related structure data
Related structure data | 1h2tC 1h2vC 1h6kS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999313, 0.020211, 0.031048), Vector: Details | ONE DIMER IS FORMED BY A HETERODIMERIC ASSOCIATIONOF CHAIN A AND CHAIN XONE DIMER IS FORMED BY A HETERODIMERIC ASSOCIATIONOF CHAIN B AND CHAIN Y | |
-Components
#1: Protein | Mass: 83835.242 Da / Num. of mol.: 2 / Fragment: MIF4G DOMAIN, RESIDUES 20-652,701-790 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A GLYCINE, ENGINEERED MUTATION ALA 479 SER Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q09161 #2: Protein | Mass: 18028.131 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P52298 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE CAP-BINDING PROTEIN (CBC) COMPLEX IS AN HETERODIMER OF CBP80 AND CBP20. CHAIN A, B ENGINEERED ...THE CAP-BINDING PROTEIN (CBC) COMPLEX IS AN HETERODIME | Sequence details | DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A ...DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A GLYCINE FOR CHAIN A,B | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.6 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 6 / Method: vapor diffusion, hanging dropDetails: Mazza, C., (2002) Acta Crystallogr.,Sect.D, 58, 2194. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 105598 / % possible obs: 89.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.6 / % possible all: 65.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 91470 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H6K Resolution: 2.4→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2384394.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 20 - 26 FROM CHAIN A AND B AR DISORDERED RESIDUES, 528 - 538 FROM CHAIN A ARE DISORDERED, RESIDUES 528 - 537 FROM CHAIN B ARE DISORDERED, RESIDUES 1-3 AND 153 - 156 FROM CHAIN X ARE ...Details: RESIDUES 20 - 26 FROM CHAIN A AND B AR DISORDERED RESIDUES, 528 - 538 FROM CHAIN A ARE DISORDERED, RESIDUES 528 - 537 FROM CHAIN B ARE DISORDERED, RESIDUES 1-3 AND 153 - 156 FROM CHAIN X ARE DISORDERED, RESIDUES 1 - 4 AND 152 - 156 FROM CHAIN Y ARE DISORDERED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4005 Å2 / ksol: 0.339272 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 91470 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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