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Open data
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Basic information
Entry | Database: PDB / ID: 4pjo | ||||||
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Title | Minimal U1 snRNP | ||||||
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![]() | SPLICING / U1 snRNP / Spliceosome / Pre-mRNA splicing / Ribonucleoprotein | ||||||
Function / homology | ![]() negative regulation of protein refolding / regulation of ATP-dependent activity / 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 ...negative regulation of protein refolding / regulation of ATP-dependent activity / 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 / U1 snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / negative regulation of chaperone-mediated autophagy / telomerase holoenzyme complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA 5'-splice site recognition / regulation of RNA splicing / U5 snRNP / spliceosomal snRNP assembly / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / single-stranded RNA binding / nuclear body / nuclear speck / mRNA binding / enzyme binding / protein homodimerization activity / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Kondo, Y. / Oubridge, C. / van Roon, A.M. / Nagai, K. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 695.8 KB | Display | ![]() |
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PDB format | ![]() | 553 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 776.6 KB | Display | ![]() |
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Full document | ![]() | 826.1 KB | Display | |
Data in XML | ![]() | 99.3 KB | Display | |
Data in CIF | ![]() | 139.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pkdC ![]() 2y9a S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
-Small nuclear ribonucleoprotein ... , 6 types, 24 molecules AaOoCcQqDdRrEeSsFfTtGgUu
#1: Protein | Mass: 13940.308 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 10026.635 Da / Num. of mol.: 4 / Mutation: M1V Source method: isolated from a genetically manipulated source Details: Expressed as a fusion protein with the N-terminal 59 residues of U1-70k protein joined via a (Gly-Ser)3 linker to its N-terminus. This fusion protein is co-expressed with SmD2. Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13551.928 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): Coexpressed with 70k-SmD1 fusion protein Production host: ![]() ![]() #5: Protein | Mass: 10817.601 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Protein | Mass: 8369.846 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #7: Protein | Mass: 8508.084 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 1 types, 4 molecules BbPp
#2: Protein | Mass: 10911.931 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-U1 small nuclear ribonucleoprotein ... , 2 types, 8 molecules KkNnLlMm
#8: Protein | Mass: 6862.841 Da / Num. of mol.: 4 / Mutation: M1G Source method: isolated from a genetically manipulated source Details: Expressed as a fusion protein with SmD1 (1-85) joined via a (Gly-Ser)3 linker at its C-terminus. This fusion protein is co-expressed with SmD2. An N-terminal tag is cleaved by TEV protease ...Details: Expressed as a fusion protein with SmD1 (1-85) joined via a (Gly-Ser)3 linker at its C-terminus. This fusion protein is co-expressed with SmD2. An N-terminal tag is cleaved by TEV protease during purification, leaving an N-terminal Gly residue. Source: (gene. exp.) ![]() ![]() ![]() #9: Protein | Mass: 7279.186 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-RNA chain , 2 types, 8 molecules 1234XxYy
#10: RNA chain | Mass: 19575.514 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Made by in vitro transcription using T7 RNA polymerase from a linearised pUC plasmid template containing a T7 promoter followed by the template sequence. Source: (synth.) ![]() #11: RNA chain | Mass: 3200.972 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: RNA made by chemical synthesis. Sequence based on consensus human 5' splice site. Source: (synth.) ![]() |
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-Non-polymers , 8 types, 83 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#12: Chemical | ChemComp-ZN / #13: Chemical | #14: Chemical | ChemComp-MG / #15: Chemical | ChemComp-K / #16: Chemical | ChemComp-EOH / | #17: Chemical | ChemComp-CL / | #18: Chemical | ChemComp-SO4 / | #19: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.7 % / Description: 0.3 x 0.04 x 0.04 mm^3 rods |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: Minimal U1 snRNP at 4 mg/ml in 300mM KCl, 20mM KHepes, pH 7.5, 5mM MgCl2, 1mM DTT, 0.15 mM polyamine-9 mixed 1:1 with 7% MPD, 180mM KCl, 5mM MgSO4, 50mM NaHepes pH 6.4. Streak seeded. Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2013 |
Radiation | Monochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→70 Å / Num. all: 80571 / Num. obs: 80571 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 172.1 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Y9A ![]() 2y9a Resolution: 3.3→70 Å / SU ML: 0.423 / Cross valid method: FREE R-VALUE / ESU R Free: 0.518
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Displacement parameters | Biso mean: 99.241 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→70 Å
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LS refinement shell | Resolution: 3.3→3.386 Å
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