+Open data
-Basic information
Entry | Database: PDB / ID: 7vpx | ||||||
---|---|---|---|---|---|---|---|
Title | The cryo-EM structure of the human pre-A complex | ||||||
Components |
| ||||||
Keywords | SPLICING / human spliceosome / pre-A complex / PRP5 / A complex / U1 snRNP / U2 snRNP | ||||||
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 / Leydig cell differentiation / histone pre-mRNA 3'end processing complex / 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 / snRNP binding / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / negative regulation of chaperone-mediated autophagy / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / 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 / SAGA complex / positive regulation of transcription by RNA polymerase III / U1 snRNP / pre-mRNA 5'-splice site binding / Cajal body / U2-type prespliceosome / intercellular bridge / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 5'-splice site recognition / 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 / 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 / negative regulation of smooth muscle cell proliferation / negative regulation of protein catabolic process / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / fibrillar center / positive regulation of neuron projection development / nuclear matrix / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / mRNA processing / transcription corepressor activity / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / RNA helicase activity / single-stranded RNA binding / chromatin remodeling / nuclear body / ribosome / RNA helicase / nuclear speck / mRNA binding / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / ATP hydrolysis activity / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) unidentified adenovirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Zhang, X. / Zhan, X. / Shi, Y. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vpx.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vpx.ent.gz | 848.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vpx_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vpx_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7vpx_validation.xml.gz | 150 KB | Display | |
Data in CIF | 7vpx_validation.cif.gz | 242.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vpx ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vpx | HTTPS FTP |
-Related structure data
Related structure data | 32074MC 7evoC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Splicing factor 3A subunit ... , 3 types, 3 molecules BAC
#1: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428 |
---|---|
#10: Protein | Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459 |
#11: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874 |
-Protein , 5 types, 6 molecules DJEfk6
#2: Protein | Mass: 68401.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15637 | ||
---|---|---|---|
#3: Protein | Mass: 29900.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75937 | ||
#12: Protein | Mass: 117576.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7L014, RNA helicase | ||
#20: Protein | Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678 #28: Protein | | Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0 |
-RNA chain , 4 types, 4 molecules HIKL
#4: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340097 |
---|---|
#22: RNA chain | Mass: 83089.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus |
#23: RNA chain | Mass: 3256.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus |
#24: RNA chain | Mass: 52697.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1781322691 |
-Splicing factor 3B subunit ... , 5 types, 5 molecules 12345
#5: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533 |
---|---|
#6: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435 |
#7: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393 |
#8: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427 |
#9: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5 |
-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules FG
#13: Protein | Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661 |
---|---|
#14: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579 |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules aibmcldnejgh
#15: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316 #16: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306 #17: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304 #18: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308 #19: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318 #21: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314 |
---|
-U1 small nuclear ribonucleoprotein ... , 3 types, 3 molecules OMN
#25: Protein | Mass: 51683.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08621 |
---|---|
#26: Protein | Mass: 31319.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09012 |
#27: Protein | Mass: 17415.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09234 |
-Non-polymers , 2 types, 7 molecules
#29: Chemical | ChemComp-ZN / #30: Chemical | ChemComp-SJT / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||
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 |
---|---|
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: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
---|---|
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 419522 / Symmetry type: POINT |
Refinement | Highest resolution: 3 Å |