+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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Function / homology | Function and homology information nuclear body organization / negative regulation of protein refolding / U2AF complex / regulation of steroid biosynthetic process / U11/U12 snRNP / regulation of ATP-dependent activity / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding ...nuclear body organization / negative regulation of protein refolding / U2AF complex / regulation of steroid biosynthetic process / U11/U12 snRNP / regulation of ATP-dependent activity / snRNP binding / U2 snRNP binding / 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 / Leydig cell differentiation / splicing factor binding / protein methylation / U12-type spliceosomal complex / methylosome / male sex determination / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / negative regulation of chaperone-mediated autophagy / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / regulation of mRNA splicing, via spliceosome / 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 / pre-mRNA 5'-splice site binding / precatalytic spliceosome / spliceosomal complex assembly / intercellular bridge / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / U5 snRNP / Cajal body / 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 / 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 / cytoplasmic ribonucleoprotein granule / mRNA processing / fibrillar center / mRNA splicing, via spliceosome / positive regulation of neuron projection development / nuclear matrix / 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 / ATP hydrolysis activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (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: To Be Published Title: Mechanism for Branch Site Recognition and Proofreading During Prespliceosome Assembly Authors: Zhang X / Zhan X / Shi Y | |||||||||
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 | 44.1 KB 44.1 KB | Display Display | EMDB header |
Images | emd_32074.png | 64.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32074 | HTTPS FTP |
-Related structure data
Related structure data | 7vpxMC 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
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
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 419522 |