+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31334 | |||||||||
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Title | The cryo-EM map of the human 17S U2 snRNP core region | |||||||||
Map data | The EM map of U2 snRNP | |||||||||
Sample |
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Keywords | U2 snRNP / PRP5 / SF3B1 / Splicing | |||||||||
Function / homology | Function and homology information U11/U12 snRNP / snRNP binding / U2 snRNP binding / chromatin-protein adaptor activity / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs ...U11/U12 snRNP / snRNP binding / U2 snRNP binding / chromatin-protein adaptor activity / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein localization to site of double-strand break / splicing factor binding / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / poly-ADP-D-ribose modification-dependent protein binding / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / U4 snRNP / U2 snRNP / SAGA complex / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / double-strand break repair via homologous recombination / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / cytoplasmic ribonucleoprotein granule / mRNA processing / fibrillar center / mRNA splicing, via spliceosome / positive regulation of neuron projection development / nuclear matrix / site of double-strand break / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / RNA helicase activity / nucleic acid binding / nuclear body / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Zhang X / Zhan X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Structural insights into branch site proofreading by human spliceosome Authors: Zhang X / Zhan X / Bian T / Yang F / Li P / Lu Y / Xing Z / Fan R / Zhang QC / Shi Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31334.map.gz | 116.7 MB | EMDB map data format | |
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Header (meta data) | emd-31334-v30.xml emd-31334.xml | 36.2 KB 36.2 KB | Display Display | EMDB header |
Images | emd_31334.png | 35.5 KB | ||
Filedesc metadata | emd-31334.cif.gz | 12.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31334 | HTTPS FTP |
-Related structure data
Related structure data | 7evoMC 7evnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31334.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The EM map of U2 snRNP | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : The human U2 snRNP
+Supramolecule #1: The human U2 snRNP
+Macromolecule #1: U2 snRNA
+Macromolecule #2: Splicing factor 3B subunit 1
+Macromolecule #3: Splicing factor 3B subunit 2
+Macromolecule #4: Splicing factor 3B subunit 3
+Macromolecule #5: Splicing factor 3B subunit 4
+Macromolecule #6: Splicing factor 3B subunit 5
+Macromolecule #7: PHD finger-like domain-containing protein 5A
+Macromolecule #8: Splicing factor 3A subunit 1
+Macromolecule #9: Splicing factor 3A subunit 2
+Macromolecule #10: Splicing factor 3A subunit 3
+Macromolecule #11: HIV Tat-specific factor 1
+Macromolecule #12: RNA helicase
+Macromolecule #13: U2 small nuclear ribonucleoprotein A'
+Macromolecule #14: U2 small nuclear ribonucleoprotein B''
+Macromolecule #15: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #16: Small nuclear ribonucleoprotein F
+Macromolecule #17: Small nuclear ribonucleoprotein E
+Macromolecule #18: Small nuclear ribonucleoprotein G
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #20: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #21: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #22: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~...
+Macromolecule #23: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Initial model from CryoSparc |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 485418 |