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Open data
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Basic information
| Entry | Database: PDB / ID: 4wzj | |||||||||
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| Title | Spliceosomal U4 snRNP core domain | |||||||||
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Keywords | SPLICING / Splicing-RNA complex / pre-mRNA splicing / snRNP biogenesis / Sm site binding | |||||||||
| Function / homology | Function and homology informationU2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation ...U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / RNA Polymerase II Transcription Termination / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / enzyme binding / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Leung, A.K.W. / Nagai, K. / Li, J. | |||||||||
Citation | Journal: Nature / Year: 2011Title: Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Authors: Leung, A.K. / Nagai, K. / Li, J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1999Title: Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Authors: Kambach, C. / Walke, S. / Young, R. / Avis, J.M. / de la Fortelle, E. / Raker, V.A. / Luhrmann, R. / Li, J. / Nagai, K. #2: Journal: Embo J. / Year: 2001Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D. #3: Journal: Elife / Year: 2015Title: Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. Authors: Kondo, Y. / Oubridge, C. / van Roon, A.M. / Nagai, K. #4: Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Re-refinement of the spliceosomal U4 snRNP core-domain structure Authors: Li, J. / Leung, A.K. / Kondo, Y. / Oubridge, C. / Nagai, K. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4wzj.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb4wzj.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 4wzj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4wzj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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| Full document | 4wzj_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | 4wzj_validation.xml.gz | 225.6 KB | Display | |
| Data in CIF | 4wzj_validation.cif.gz | 325.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/4wzj ftp://data.pdbj.org/pub/pdb/validation_reports/wz/4wzj | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4pjoS S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
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Components
-Small nuclear ribonucleoprotein ... , 6 types, 72 molecules AHOAAHHOOAAAHHHOOOAAAAHHHHOOOOCJQCCJJQQCCCJJJQQQCCCCJJJJQQQQDKRDDKKRR...
| #1: Protein | Mass: 13783.114 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered, co-expressed with SM B / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD3 / Plasmid: PQE30 / Details (production host): co-expressed with Sm B / Production host: ![]() #3: Protein | Mass: 13153.460 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered, co-expressed with SM D2 / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Plasmid: PET / Details (production host): COEXPRESSED WITH SM-D2 / Production host: ![]() #4: Protein | Mass: 13551.928 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered, co-expressed with SM D1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2 / Plasmid: PET / Details (production host): COEXPRESSED WITH SM-D1 / Production host: ![]() #5: Protein | Mass: 9734.171 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered, co-expressed with SM E and SM G / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Plasmid: PET15B / Details (production host): Co-expressed with Sm E and Sm G / Production host: ![]() #6: Protein | Mass: 10817.601 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered, co-expressed with SM F and SM G / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Plasmid: PET15B / Details (production host): Co-expressed with SmF and Sm G / Production host: ![]() #7: Protein | Mass: 8508.084 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered, co-expressed with SM E and SM F / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Plasmid: PET15B / Details (production host): Co-expressed with SmE and SmF / Production host: ![]() |
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-Protein / RNA chain / Non-polymers , 3 types, 27 molecules BIPBBIIPPBBBIIIPPPBBBBIIIIPPPPVXYVVXXYYVVVXXXYYYVVVVXXXXYYYY

| #2: Protein | Mass: 10911.931 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: engineered; residues 1-95 of sequence expressed, co-expressed with SM D3 Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPB, COD, SNRPB1 / Plasmid: PQE30 / Details (production host): co-expressed with Sm D3 / Production host: ![]() #8: RNA chain | Mass: 21957.041 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE / Source: (gene. exp.) Homo sapiens (human) / Gene: RNU4-1 / Production host: synthetic construct (others)#9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION |
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Sample preparation
| Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 63 % / Description: hexagonal bipyramid |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 4-10% PEG 550 MME, 0.1M KSCN or (NH4)2SO4, 0.1 M TRIS PH 8.0-8.5 10 MM MGCL2, 2 MM CYCLEN. PH range: 8.0-8.5 |
-Data collection
| Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
| Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2004 | ||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
| Reflection twin |
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| Reflection | Resolution: 3.59→66.16 Å / Num. all: 202467 / Num. obs: 202467 / % possible obs: 82.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 3.3 | ||||||||||||||||||||||||||||||
| Reflection shell | Resolution: 3.59→3.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.1 / % possible all: 20.8 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 4PJO Resolution: 3.6→66.154 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.164 / Data cutoff high absF: 0 / Data cutoff low absF: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.124 Details: Hydrogens have been added in their riding positions
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 128.369 Å2
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| Refinement step | Cycle: LAST / Resolution: 3.6→66.154 Å
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| Refine LS restraints |
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Homo sapiens (human)
X-RAY DIFFRACTION
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