9QDQ
Cryo-EM structure of Upf1-Nmd4-Ebs1 in complex with RNA
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000184 | biological_process | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay |
| A | 0000956 | biological_process | nuclear-transcribed mRNA catabolic process |
| A | 0003678 | molecular_function | DNA helicase activity |
| A | 0003697 | molecular_function | single-stranded DNA binding |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003724 | molecular_function | RNA helicase activity |
| A | 0003729 | molecular_function | mRNA binding |
| A | 0004386 | molecular_function | helicase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006310 | biological_process | DNA recombination |
| A | 0006449 | biological_process | regulation of translational termination |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0008298 | biological_process | intracellular mRNA localization |
| A | 0016567 | biological_process | protein ubiquitination |
| A | 0016887 | molecular_function | ATP hydrolysis activity |
| A | 0030466 | biological_process | silent mating-type cassette heterochromatin formation |
| A | 0032574 | molecular_function | 5'-3' RNA helicase activity |
| A | 0033678 | molecular_function | 5'-3' DNA/RNA helicase activity |
| A | 0036121 | molecular_function | double-stranded DNA helicase activity |
| A | 0043024 | molecular_function | ribosomal small subunit binding |
| A | 0043139 | molecular_function | 5'-3' DNA helicase activity |
| A | 0070478 | biological_process | nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay |
| A | 0071026 | biological_process | cytoplasmic RNA surveillance |
| B | 0000184 | biological_process | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay |
| B | 0000781 | cellular_component | chromosome, telomeric region |
| B | 0000932 | cellular_component | P-body |
| B | 0003674 | molecular_function | molecular_function |
| B | 0005634 | cellular_component | nucleus |
| B | 0005697 | cellular_component | telomerase holoenzyme complex |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006310 | biological_process | DNA recombination |
| B | 0017148 | biological_process | negative regulation of translation |
| B | 0042162 | molecular_function | telomeric repeat DNA binding |
| B | 0070034 | molecular_function | telomerase RNA binding |
| C | 0000184 | biological_process | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay |
| C | 0003674 | molecular_function | molecular_function |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 226 |
| Details | Domain: {"description":"UPF1-type SF1B helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU01433","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 212 |
| Details | Domain: {"description":"UPF1-type SF1B helicase C-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU01433","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 32 |
| Details | Region: {"description":"C3H","evidences":[{"source":"PROSITE-ProRule","id":"PRU01341","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 28 |
| Details | Region: {"description":"CC/SHH/C","evidences":[{"source":"PROSITE-ProRule","id":"PRU01341","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 30 |
| Details | Region: {"description":"C4","evidences":[{"source":"PROSITE-ProRule","id":"PRU01341","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 630 |
| Details | Region: {"description":"Helicase domain","evidences":[{"source":"PubMed","id":"30218034","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 132 |
| Details | Region: {"description":"Helicase subdomain 1B","evidences":[{"source":"PubMed","id":"30218034","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 62 |
| Details | Region: {"description":"Helicase subdomain 1C","evidences":[{"source":"PubMed","id":"30218034","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01341","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21419344","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2XZL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 11 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"21419344","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2XZL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"2XZL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
