+Open data
-Basic information
Entry | Database: PDB / ID: 8rc0 | ||||||
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Title | Structure of the human 20S U5 snRNP | ||||||
Components |
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Keywords | SPLICING / snRNP / CD2BP2 / spliceosome / U5 | ||||||
Function / homology | Function and homology information RNA localization / R-loop processing / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...RNA localization / R-loop processing / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing 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 / Cajal body / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / helicase activity / spliceosomal complex / fibrillar center / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / protein-macromolecule adaptor activity / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / cellular response to lipopolysaccharide / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / chromatin / nucleolus / GTP binding / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Schneider, S. / Galej, W.P. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of the human 20S U5 snRNP. Authors: Sarah Schneider / Irina Brandina / Daniel Peter / Sonal Lagad / Angelique Fraudeau / Júlia Portell-Montserrat / Jonas Tholen / Jiangfeng Zhao / Wojciech P Galej / Abstract: The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. ...The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rc0.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rc0.ent.gz | 841.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rc0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8rc0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8rc0_validation.xml.gz | 151 KB | Display | |
Data in CIF | 8rc0_validation.cif.gz | 250.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/8rc0 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/8rc0 | HTTPS FTP |
-Related structure data
Related structure data | 19041MC 8q91C 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
-Protein , 6 types, 6 molecules FAEDhC
#1: Protein | Mass: 37687.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD2BP2 / Production host: Homo sapiens (human) / References: UniProt: O95400 |
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#2: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9 |
#4: Protein | Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906 |
#5: Protein | Mass: 95785.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX23 / Production host: Homo sapiens (human) / References: UniProt: Q9BUQ8 |
#14: Protein | Mass: 24642.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPB, COD, SNRPB1 / Production host: Homo sapiens (human) / References: UniProt: P14678 |
#15: Protein | Mass: 109560.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EFTUD2, KIAA0031, SNRP116 / Production host: Homo sapiens (human) / References: UniProt: Q15029 |
-U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules GB
#6: Protein | Mass: 39359.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP40, PRP8BP, SFP38, WDR57 / Production host: Homo sapiens (human) / References: UniProt: Q96DI7 |
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#7: Protein | Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase |
-Small nuclear ribonucleoprotein ... , 6 types, 6 molecules iklmnj
#8: Protein | Mass: 13310.653 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Production host: Homo sapiens (human) / References: UniProt: P62314 |
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#9: Protein | Mass: 13940.308 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD3 / Production host: Homo sapiens (human) / References: UniProt: P62318 |
#10: Protein | Mass: 10817.601 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Production host: Homo sapiens (human) / References: UniProt: P62304 |
#11: Protein | Mass: 9734.171 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Production host: Homo sapiens (human) / References: UniProt: P62306 |
#12: Protein | Mass: 8508.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Homo sapiens (human) / References: UniProt: P62308 |
#13: Protein | Mass: 13551.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2, SNRPD1 / Production host: Homo sapiens (human) / References: UniProt: P62316 |
-RNA chain / Non-polymers , 2 types, 2 molecules 5
#16: Chemical | ChemComp-GTP / |
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#3: 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 |
-Details
Has ligand of interest | Y |
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-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: 20S U5 snRNP complex purified from HEK293F cell line / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: objective aperture 70 um |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.2 sec. / Electron dose: 40.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8506 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 490503 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237698 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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