+
Open data
-
Basic information
Entry | Database: PDB / ID: 4wzj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Spliceosomal U4 snRNP core domain | |||||||||
![]() |
| |||||||||
![]() | SPLICING / Splicing-RNA complex / pre-mRNA splicing / snRNP biogenesis / Sm site binding | |||||||||
Function / homology | ![]() 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 / methylosome ...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 / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leung, A.K.W. / Nagai, K. / Li, J. | |||||||||
![]() | ![]() Title: Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Authors: Leung, A.K. / Nagai, K. / Li, J. #1: ![]() Title: 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: ![]() Title: 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: ![]() Title: 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4pjoS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
-
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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() |
---|
-Protein / RNA chain / Non-polymers , 3 types, 27 molecules BIPBBIIPPBBBIIIPPPBBBBIIIIPPPPVXYVVXXYYVVVXXXYYYVVVVXXXXYYYY![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#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.) ![]() ![]() ![]() #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.) ![]() #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 63 % / Description: hexagonal bipyramid |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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 |
| ||||||||||||||||||||||||||||||
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 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→66.154 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|