+Open data
-Basic information
Entry | Database: PDB / ID: 3pgw | ||||||
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Title | Crystal structure of human U1 snRNP | ||||||
Components |
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Keywords | splicing/DNA/RNA / PROTEIN-RNA COMPLEX / U1 snRNA / Sm fold / Sm core / RRM / Splicing / mRNA / snRNPs / splicing factors / splicing-DNA-RNA complex | ||||||
Function / homology | Function and homology information negative regulation of protein refolding / histone mRNA metabolic process / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / import into nucleus / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs ...negative regulation of protein refolding / histone mRNA metabolic process / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / import into nucleus / 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 / negative regulation of chaperone-mediated autophagy / 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 / positive regulation of mRNA splicing, via spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / termination of RNA polymerase II transcription / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / 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 / nuclear speck / ribonucleoprotein complex / mRNA binding / enzyme binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, MIRAS / Resolution: 4.4 Å | ||||||
Authors | Weber, G. / Trowitzsch, S. / Kastner, B. / Luehrmann, R. / Wahl, M.C. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Functional organization of the Sm core in the crystal structure of human U1 snRNP. Authors: Weber, G. / Trowitzsch, S. / Kastner, B. / Luhrmann, R. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pgw.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pgw.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pgw_validation.pdf.gz | 462.1 KB | Display | wwPDB validaton report |
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Full document | 3pgw_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 3pgw_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 3pgw_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/3pgw ftp://data.pdbj.org/pub/pdb/validation_reports/pg/3pgw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | biological assembly 1: chains A, S, Z, B, X, Y, F, E, G, R, D / biological assembly 2: chains P, L ,W, Q, U, V, I, H, J, N, M |
-Components
-Protein , 9 types, 18 molecules APSLZWBQXUYVFIEHGJ
#1: Protein | Mass: 31319.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P09012 #2: Protein | Mass: 51683.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P08621 #3: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62318 #4: Protein | Mass: 23686.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q66K91, UniProt: P14678*PLUS #5: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62314 #6: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62316 #7: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62306 #8: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62304 #9: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: D6W5G6, UniProt: P62308*PLUS |
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-RNA chain / DNA chain , 2 types, 4 molecules RNDM
#10: RNA chain | Mass: 52697.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA #11: DNA chain | Mass: 2803.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA oligonucleotide |
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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: 2.39 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 8-10% PEG 4000, 0.1 M Trisodium citrate, 2 mM EDTA, 100 mM NaCl, 1-2% Anapoe X-305, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2007 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 4.4→100 Å / Num. all: 28274 / Num. obs: 28079 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 4.4→4.6 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 3480 / Rsym value: 0.73 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, MIRAS / Resolution: 4.4→100 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 4.4→100 Å
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Refine LS restraints |
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