+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32074 | |||||||||
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Title | The cryo-EM structure of the human pre-A complex | |||||||||
Map data | The cryo-EM map for the U2 part of human pre-A complex | |||||||||
Sample |
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Keywords | human spliceosome / pre-A complex / PRP5 / A complex / U1 snRNP / U2 snRNP / SPLICING | |||||||||
Function / homology | Function and homology information nuclear body organization / negative regulation of protein refolding / U2AF complex / regulation of steroid biosynthetic process / regulation of ATP-dependent activity / U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP ...nuclear body organization / negative regulation of protein refolding / U2AF complex / regulation of steroid biosynthetic process / regulation of ATP-dependent activity / U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / Leydig cell differentiation / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / male sex determination / 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 / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / negative regulation of chaperone-mediated autophagy / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / intercellular bridge / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / regulation of RNA splicing / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Hsp70 protein binding / 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 / negative regulation of smooth muscle cell proliferation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA processing / fibrillar center / nuclear matrix / cytoplasmic ribonucleoprotein granule / positive regulation of neuron projection development / mRNA splicing, via spliceosome / transcription corepressor activity / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / RNA helicase activity / single-stranded RNA binding / nuclear body / ribosome / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified adenovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zhang X / Zhan X / Shi Y | |||||||||
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: Xiaofeng Zhang / Xiechao Zhan / Tong Bian / Fenghua Yang / Pan Li / Yichen Lu / Zhihan Xing / Rongyan Fan / Qiangfeng Cliff Zhang / Yigong Shi / Abstract: Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the ...Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32074.map.gz | 398.8 MB | EMDB map data format | |
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Header (meta data) | emd-32074-v30.xml emd-32074.xml | 47.3 KB 47.3 KB | Display Display | EMDB header |
Images | emd_32074.png | 64.2 KB | ||
Filedesc metadata | emd-32074.cif.gz | 13.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32074 | HTTPS FTP |
-Validation report
Summary document | emd_32074_validation.pdf.gz | 468.1 KB | Display | EMDB validaton report |
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Full document | emd_32074_full_validation.pdf.gz | 467.7 KB | Display | |
Data in XML | emd_32074_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_32074_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32074 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32074 | HTTPS FTP |
-Related structure data
Related structure data | 7vpxMC 7evoC 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_32074.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The cryo-EM map for the U2 part of human pre-A complex | ||||||||||||||||||||
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 : human pre-A complex
+Supramolecule #1: human pre-A complex
+Supramolecule #2: human pre-A
+Supramolecule #3: pre-mRNA, 5SS
+Macromolecule #1: Splicing factor 3A subunit 2
+Macromolecule #2: Splicing factor 1
+Macromolecule #3: DnaJ homolog subfamily C member 8
+Macromolecule #5: Splicing factor 3B subunit 1
+Macromolecule #6: Splicing factor 3B subunit 2
+Macromolecule #7: Splicing factor 3B subunit 3
+Macromolecule #8: Splicing factor 3B subunit 4
+Macromolecule #9: Splicing factor 3B subunit 5
+Macromolecule #10: Splicing factor 3A subunit 1
+Macromolecule #11: Splicing factor 3A subunit 3
+Macromolecule #12: Probable ATP-dependent RNA helicase DDX46
+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 #25: U1 small nuclear ribonucleoprotein 70 kDa
+Macromolecule #26: U1 small nuclear ribonucleoprotein A
+Macromolecule #27: U1 small nuclear ribonucleoprotein C
+Macromolecule #28: PHD finger-like domain-containing protein 5A
+Macromolecule #4: U2 snRNA
+Macromolecule #22: pre-mRNA
+Macromolecule #23: 5SS
+Macromolecule #24: U1 snRNA
+Macromolecule #29: ZINC ION
+Macromolecule #30: spliceostatin A (form II)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 419522 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |