7EVN
The cryo-EM structure of the DDX42-SF3b complex
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000375 | biological_process | RNA splicing, via transesterification reactions |
| A | 0000387 | biological_process | spliceosomal snRNP assembly |
| A | 0000388 | biological_process | spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) |
| A | 0000398 | biological_process | mRNA splicing, via spliceosome |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005681 | cellular_component | spliceosomal complex |
| A | 0005684 | cellular_component | U2-type spliceosomal complex |
| A | 0005686 | cellular_component | U2 snRNP |
| A | 0005689 | cellular_component | U12-type spliceosomal complex |
| A | 0005730 | cellular_component | nucleolus |
| A | 0006282 | biological_process | regulation of DNA repair |
| A | 0006397 | biological_process | mRNA processing |
| A | 0008380 | biological_process | RNA splicing |
| A | 0030620 | molecular_function | U2 snRNA binding |
| A | 0042177 | biological_process | negative regulation of protein catabolic process |
| A | 0043484 | biological_process | regulation of RNA splicing |
| A | 0044877 | molecular_function | protein-containing complex binding |
| A | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| A | 0071005 | cellular_component | U2-type precatalytic spliceosome |
| A | 0071013 | cellular_component | catalytic step 2 spliceosome |
| A | 1903241 | biological_process | U2-type prespliceosome assembly |
| B | 0000387 | biological_process | spliceosomal snRNP assembly |
| B | 0000388 | biological_process | spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) |
| B | 0000398 | biological_process | mRNA splicing, via spliceosome |
| B | 0003723 | molecular_function | RNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005681 | cellular_component | spliceosomal complex |
| B | 0005684 | cellular_component | U2-type spliceosomal complex |
| B | 0005686 | cellular_component | U2 snRNP |
| B | 0005689 | cellular_component | U12-type spliceosomal complex |
| B | 0006282 | biological_process | regulation of DNA repair |
| B | 0006397 | biological_process | mRNA processing |
| B | 0008380 | biological_process | RNA splicing |
| B | 0043484 | biological_process | regulation of RNA splicing |
| B | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| B | 0071005 | cellular_component | U2-type precatalytic spliceosome |
| B | 0071011 | cellular_component | precatalytic spliceosome |
| B | 1903241 | biological_process | U2-type prespliceosome assembly |
| B | 1990935 | molecular_function | splicing factor binding |
| C | 0000245 | biological_process | spliceosomal complex assembly |
| C | 0003729 | molecular_function | mRNA binding |
| D | 0000387 | biological_process | spliceosomal snRNP assembly |
| D | 0000388 | biological_process | spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) |
| D | 0000398 | biological_process | mRNA splicing, via spliceosome |
| D | 0003677 | molecular_function | DNA binding |
| D | 0003723 | molecular_function | RNA binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005681 | cellular_component | spliceosomal complex |
| D | 0005684 | cellular_component | U2-type spliceosomal complex |
| D | 0005686 | cellular_component | U2 snRNP |
| D | 0005689 | cellular_component | U12-type spliceosomal complex |
| D | 0006351 | biological_process | DNA-templated transcription |
| D | 0006397 | biological_process | mRNA processing |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0008380 | biological_process | RNA splicing |
| D | 0016363 | cellular_component | nuclear matrix |
| D | 0016607 | cellular_component | nuclear speck |
| D | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0048863 | biological_process | stem cell differentiation |
| D | 0071005 | cellular_component | U2-type precatalytic spliceosome |
| D | 0071011 | cellular_component | precatalytic spliceosome |
| D | 1903241 | biological_process | U2-type prespliceosome assembly |
| E | 0000166 | molecular_function | nucleotide binding |
| E | 0003676 | molecular_function | nucleic acid binding |
| E | 0003723 | molecular_function | RNA binding |
| E | 0003724 | molecular_function | RNA helicase activity |
| E | 0004386 | molecular_function | helicase activity |
| E | 0005515 | molecular_function | protein binding |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0008104 | biological_process | intracellular protein localization |
| E | 0015030 | cellular_component | Cajal body |
| E | 0016020 | cellular_component | membrane |
| E | 0016607 | cellular_component | nuclear speck |
| E | 0016787 | molecular_function | hydrolase activity |
| E | 0016887 | molecular_function | ATP hydrolysis activity |
| E | 0042981 | biological_process | regulation of apoptotic process |
| E | 0071004 | cellular_component | U2-type prespliceosome |
| E | 1903241 | biological_process | U2-type prespliceosome assembly |
Functional Information from PROSITE/UniProt
| site_id | PS00039 |
| Number of Residues | 9 |
| Details | DEAD_ATP_HELICASE DEAD-box subfamily ATP-dependent helicases signature. VFDEADRmF |
| Chain | Residue | Details |
| E | VAL405-PHE413 |
| site_id | PS00290 |
| Number of Residues | 7 |
| Details | IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. FVCSATH |
| Chain | Residue | Details |
| A | PHE287-HIS293 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 77 |
| Details | Region: {"description":"Interaction with SF3B1 and SF3B3","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | Site: {"description":"Interaction with RNA","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17525332","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 39 |
| Details | Repeat: {"description":"HEAT 1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 34 |
| Details | Repeat: {"description":"HEAT 2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 37 |
| Details | Repeat: {"description":"HEAT 3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 34 |
| Details | Repeat: {"description":"HEAT 4"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 5"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 6"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 7"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 8"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 9"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 10"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 38 |
| Details | Repeat: {"description":"HEAT 11"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 39 |
| Details | Region: {"description":"Interaction with SF3B14"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | Region: {"description":"Interaction with PHF5A","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 56 |
| Details | Region: {"description":"Interaction with SF3B3 and SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI19 |
| Number of Residues | 1 |
| Details | Site: {"description":"Interaction with PHF5A","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI20 |
| Number of Residues | 4 |
| Details | Site: {"description":"Interaction with SF3B3","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI21 |
| Number of Residues | 3 |
| Details | Region: {"description":"Interaction with SF3B3","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI22 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"28541300","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5IFE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5SYB","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI24 |
| Number of Residues | 37 |
| Details | Region: {"description":"Interaction with PHF5A, SF3B1 and SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI25 |
| Number of Residues | 56 |
| Details | Region: {"description":"Interaction with SF3B1 and SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI26 |
| Number of Residues | 21 |
| Details | Region: {"description":"Interaction with SF3B1","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI27 |
| Number of Residues | 23 |
| Details | Region: {"description":"Interaction with SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI28 |
| Number of Residues | 5 |
| Details | Site: {"description":"Interaction with SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI29 |
| Number of Residues | 2 |
| Details | Site: {"description":"Interaction with SF3B1","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI30 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI31 |
| Number of Residues | 175 |
| Details | Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI32 |
| Number of Residues | 28 |
| Details | Motif: {"description":"Q motif"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI33 |
| Number of Residues | 3 |
| Details | Motif: {"description":"DEAD box"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI34 |
| Number of Residues | 7 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
