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Yorodumi- PDB-8q7n: cryo-EM structure of the human spliceosomal B complex protomer (t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q7n | ||||||
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Title | cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) | ||||||
Components |
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Keywords | SPLICING / spliceosome / pre-catalytic spliceosome / spliceosomal B complex | ||||||
Function / homology | Function and homology information microfibril / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / box C/D sno(s)RNA binding ...microfibril / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / box C/D sno(s)RNA binding / positive regulation of primary miRNA processing / dense fibrillar component / transcription elongation factor activity / U4/U6 snRNP / positive regulation of androgen receptor activity / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / ubiquitin-like protein conjugating enzyme binding / U4 snRNP / RNA polymerase binding / box C/D snoRNP assembly / U2 snRNP / rRNA modification in the nucleus and cytosol / positive regulation of protein targeting to mitochondrion / U3 snoRNA binding / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of miRNA metabolic process / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / regulation of alternative mRNA splicing, via spliceosome / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / RNA processing / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / ribonucleoprotein complex binding / pre-mRNA intronic binding / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor coactivator activity / response to cocaine / maturation of LSU-rRNA / maturation of SSU-rRNA / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / small-subunit processome / transcription coregulator activity / spliceosomal complex / protein modification process / mRNA processing / mRNA splicing, via spliceosome / protein tag activity / transcription corepressor activity / cellular response to xenobiotic stimulus / protein-macromolecule adaptor activity / cellular response to tumor necrosis factor / ribosomal small subunit biogenesis / ATPase binding / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / cytosolic large ribosomal subunit / transcription coactivator activity / nuclear speck / cell cycle / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / chromatin / nucleolus / GTP binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Zhang, Z. / Kumar, V. / Dybkov, O. / Will, C.L. / Urlaub, H. / Stark, H. / Luehrmann, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: New insights into the functions of B complex proteins revealed by cryo-EM of dimerized spliceosomes Authors: Zhang, Z. / Kumar, V. / Dybkov, O. / Will, C.L. / Urlaub, H. / Stark, H. / Luehrmann, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q7n.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8q7n.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8q7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q7n_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8q7n_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8q7n_validation.xml.gz | 182.5 KB | Display | |
Data in CIF | 8q7n_validation.cif.gz | 289.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/8q7n ftp://data.pdbj.org/pub/pdb/validation_reports/q7/8q7n | HTTPS FTP |
-Related structure data
Related structure data | 18225MC 8qo9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules 56Z4
#1: RNA chain | Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981 |
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#2: RNA chain | Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_004394.1 |
#11: RNA chain | Mass: 111300.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#20: RNA chain | Mass: 46528.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-Protein , 14 types, 14 molecules 7CDIKMQXrsNAST
#3: Protein | Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459 |
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#4: Protein | Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029 |
#5: Protein | Mass: 16807.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83876 |
#6: Protein | Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NAV1 |
#7: Protein | Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55081 |
#8: Protein | Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769 |
#9: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223 |
#10: Protein | Mass: 42575.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75554 |
#12: Protein | Mass: 23664.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96NC0 |
#13: Protein | Mass: 8560.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZL1 |
#16: Protein | Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906 |
#17: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9 |
#18: Protein | Mass: 90414.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43290 |
#19: Protein | Mass: 124083.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14776 |
-U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules LFJ
#14: Protein | Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3 |
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#15: Protein | Mass: 58536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43172 |
#21: Protein | Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43395 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human pre-catalytic spliceosome / Type: COMPLEX / Entity ID: #1-#11, #13-#20, #12, #21 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251564 / Symmetry type: POINT |