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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6FSZ

Structure of the nuclear RNA exosome

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
AA0000176cellular_componentnuclear exosome (RNase complex)
AA0000177cellular_componentcytoplasmic exosome (RNase complex)
AA0000178cellular_componentexosome (RNase complex)
AA0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
AA0003674molecular_functionmolecular_function
AA0003723molecular_functionRNA binding
AA0005515molecular_functionprotein binding
AA0005634cellular_componentnucleus
AA0005730cellular_componentnucleolus
AA0005737cellular_componentcytoplasm
AA0006364biological_processrRNA processing
AA0006396biological_processRNA processing
AA0006401biological_processRNA catabolic process
AA0016075biological_processrRNA catabolic process
AA0034473biological_processU1 snRNA 3'-end processing
AA0034475biological_processU4 snRNA 3'-end processing
AA0034476biological_processU5 snRNA 3'-end processing
AA0035925molecular_functionmRNA 3'-UTR AU-rich region binding
AA0071028biological_processnuclear mRNA surveillance
AA0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
AA0071038biological_processTRAMP-dependent tRNA surveillance pathway
BB0000176cellular_componentnuclear exosome (RNase complex)
BB0000177cellular_componentcytoplasmic exosome (RNase complex)
BB0000178cellular_componentexosome (RNase complex)
BB0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
BB0000956biological_processnuclear-transcribed mRNA catabolic process
BB0003674molecular_functionmolecular_function
BB0003723molecular_functionRNA binding
BB0005515molecular_functionprotein binding
BB0005634cellular_componentnucleus
BB0005730cellular_componentnucleolus
BB0005737cellular_componentcytoplasm
BB0006364biological_processrRNA processing
BB0006396biological_processRNA processing
BB0006401biological_processRNA catabolic process
BB0016075biological_processrRNA catabolic process
BB0034473biological_processU1 snRNA 3'-end processing
BB0034475biological_processU4 snRNA 3'-end processing
BB0034476biological_processU5 snRNA 3'-end processing
BB0070478biological_processnuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
BB0071028biological_processnuclear mRNA surveillance
BB0071038biological_processTRAMP-dependent tRNA surveillance pathway
BB0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
BB0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
CC0000176cellular_componentnuclear exosome (RNase complex)
CC0000177cellular_componentcytoplasmic exosome (RNase complex)
CC0000178cellular_componentexosome (RNase complex)
CC0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
CC0000956biological_processnuclear-transcribed mRNA catabolic process
CC0003674molecular_functionmolecular_function
CC0003723molecular_functionRNA binding
CC0005515molecular_functionprotein binding
CC0005634cellular_componentnucleus
CC0005654cellular_componentnucleoplasm
CC0005730cellular_componentnucleolus
CC0005737cellular_componentcytoplasm
CC0006364biological_processrRNA processing
CC0006396biological_processRNA processing
CC0006397biological_processmRNA processing
CC0006401biological_processRNA catabolic process
CC0006402biological_processmRNA catabolic process
CC0016072biological_processrRNA metabolic process
CC0016075biological_processrRNA catabolic process
CC0034473biological_processU1 snRNA 3'-end processing
CC0034475biological_processU4 snRNA 3'-end processing
CC0034476biological_processU5 snRNA 3'-end processing
CC0035925molecular_functionmRNA 3'-UTR AU-rich region binding
CC0071028biological_processnuclear mRNA surveillance
CC0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
CC0071038biological_processTRAMP-dependent tRNA surveillance pathway
CC0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
DD0000176cellular_componentnuclear exosome (RNase complex)
DD0000177cellular_componentcytoplasmic exosome (RNase complex)
DD0000178cellular_componentexosome (RNase complex)
DD0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
DD0003674molecular_functionmolecular_function
DD0003723molecular_functionRNA binding
DD0005515molecular_functionprotein binding
DD0005634cellular_componentnucleus
DD0005730cellular_componentnucleolus
DD0005737cellular_componentcytoplasm
DD0006364biological_processrRNA processing
DD0006396biological_processRNA processing
DD0006401biological_processRNA catabolic process
DD0016075biological_processrRNA catabolic process
DD0034475biological_processU4 snRNA 3'-end processing
DD0071028biological_processnuclear mRNA surveillance
DD0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
DD0071038biological_processTRAMP-dependent tRNA surveillance pathway
DD0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
DD0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
EE0000176cellular_componentnuclear exosome (RNase complex)
EE0000177cellular_componentcytoplasmic exosome (RNase complex)
EE0000178cellular_componentexosome (RNase complex)
EE0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
EE0003674molecular_functionmolecular_function
EE0003723molecular_functionRNA binding
EE0005515molecular_functionprotein binding
EE0005634cellular_componentnucleus
EE0005730cellular_componentnucleolus
EE0005737cellular_componentcytoplasm
EE0006364biological_processrRNA processing
EE0006396biological_processRNA processing
EE0006401biological_processRNA catabolic process
EE0016075biological_processrRNA catabolic process
EE0034473biological_processU1 snRNA 3'-end processing
EE0034475biological_processU4 snRNA 3'-end processing
EE0034476biological_processU5 snRNA 3'-end processing
EE0035925molecular_functionmRNA 3'-UTR AU-rich region binding
EE0071028biological_processnuclear mRNA surveillance
EE0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
EE0071038biological_processTRAMP-dependent tRNA surveillance pathway
FF0000176cellular_componentnuclear exosome (RNase complex)
FF0000177cellular_componentcytoplasmic exosome (RNase complex)
FF0000178cellular_componentexosome (RNase complex)
FF0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
FF0003674molecular_functionmolecular_function
FF0003723molecular_functionRNA binding
FF0005515molecular_functionprotein binding
FF0005634cellular_componentnucleus
FF0005730cellular_componentnucleolus
FF0005737cellular_componentcytoplasm
FF0006364biological_processrRNA processing
FF0006396biological_processRNA processing
FF0006401biological_processRNA catabolic process
FF0016075biological_processrRNA catabolic process
FF0034475biological_processU4 snRNA 3'-end processing
FF0071028biological_processnuclear mRNA surveillance
FF0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
FF0071038biological_processTRAMP-dependent tRNA surveillance pathway
FF0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
FF0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
GG0000176cellular_componentnuclear exosome (RNase complex)
GG0000177cellular_componentcytoplasmic exosome (RNase complex)
GG0000178cellular_componentexosome (RNase complex)
GG0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GG0000956biological_processnuclear-transcribed mRNA catabolic process
GG0003723molecular_functionRNA binding
GG0005515molecular_functionprotein binding
GG0005634cellular_componentnucleus
GG0005730cellular_componentnucleolus
GG0005737cellular_componentcytoplasm
GG0006364biological_processrRNA processing
GG0006396biological_processRNA processing
GG0006401biological_processRNA catabolic process
GG0030145molecular_functionmanganese ion binding
GG0034475biological_processU4 snRNA 3'-end processing
GG0071034biological_processCUT catabolic process
GG0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
GG0071038biological_processTRAMP-dependent tRNA surveillance pathway
GG0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
HH0000176cellular_componentnuclear exosome (RNase complex)
HH0000177cellular_componentcytoplasmic exosome (RNase complex)
HH0000178cellular_componentexosome (RNase complex)
HH0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
HH0000956biological_processnuclear-transcribed mRNA catabolic process
HH0003674molecular_functionmolecular_function
HH0003723molecular_functionRNA binding
HH0005515molecular_functionprotein binding
HH0005634cellular_componentnucleus
HH0005730cellular_componentnucleolus
HH0005737cellular_componentcytoplasm
HH0006364biological_processrRNA processing
HH0006396biological_processRNA processing
HH0006401biological_processRNA catabolic process
HH0034475biological_processU4 snRNA 3'-end processing
HH0071028biological_processnuclear mRNA surveillance
HH0071034biological_processCUT catabolic process
HH0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
HH0071038biological_processTRAMP-dependent tRNA surveillance pathway
HH0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
II0000176cellular_componentnuclear exosome (RNase complex)
II0000177cellular_componentcytoplasmic exosome (RNase complex)
II0000178cellular_componentexosome (RNase complex)
II0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
II0000956biological_processnuclear-transcribed mRNA catabolic process
II0003674molecular_functionmolecular_function
II0003723molecular_functionRNA binding
II0005515molecular_functionprotein binding
II0005634cellular_componentnucleus
II0005730cellular_componentnucleolus
II0005737cellular_componentcytoplasm
II0006364biological_processrRNA processing
II0006396biological_processRNA processing
II0006397biological_processmRNA processing
II0006401biological_processRNA catabolic process
II0070481biological_processnuclear-transcribed mRNA catabolic process, non-stop decay
II0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
II0071038biological_processTRAMP-dependent tRNA surveillance pathway
JJ0000049molecular_functiontRNA binding
JJ0000175molecular_function3'-5'-RNA exonuclease activity
JJ0000176cellular_componentnuclear exosome (RNase complex)
JJ0000177cellular_componentcytoplasmic exosome (RNase complex)
JJ0000178cellular_componentexosome (RNase complex)
JJ0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
JJ0003676molecular_functionnucleic acid binding
JJ0003723molecular_functionRNA binding
JJ0004518molecular_functionnuclease activity
JJ0004519molecular_functionendonuclease activity
JJ0004521molecular_functionRNA endonuclease activity
JJ0004527molecular_functionexonuclease activity
JJ0004540molecular_functionRNA nuclease activity
JJ0005515molecular_functionprotein binding
JJ0005634cellular_componentnucleus
JJ0005730cellular_componentnucleolus
JJ0005737cellular_componentcytoplasm
JJ0005739cellular_componentmitochondrion
JJ0006364biological_processrRNA processing
JJ0006396biological_processRNA processing
JJ0006397biological_processmRNA processing
JJ0006401biological_processRNA catabolic process
JJ0016075biological_processrRNA catabolic process
JJ0016787molecular_functionhydrolase activity
JJ0043628biological_processregulatory ncRNA 3'-end processing
JJ0070651biological_processnonfunctional rRNA decay
JJ0071028biological_processnuclear mRNA surveillance
JJ0071031biological_processnuclear mRNA surveillance of mRNA 3'-end processing
JJ0071034biological_processCUT catabolic process
JJ0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
JJ0071038biological_processTRAMP-dependent tRNA surveillance pathway
JJ0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
KK0000166molecular_functionnucleotide binding
KK0000175molecular_function3'-5'-RNA exonuclease activity
KK0000176cellular_componentnuclear exosome (RNase complex)
KK0000178cellular_componentexosome (RNase complex)
KK0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
KK0000973biological_processpost-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
KK0003676molecular_functionnucleic acid binding
KK0003723molecular_functionRNA binding
KK0003727molecular_functionsingle-stranded RNA binding
KK0004518molecular_functionnuclease activity
KK0004527molecular_functionexonuclease activity
KK0005515molecular_functionprotein binding
KK0005634cellular_componentnucleus
KK0005730cellular_componentnucleolus
KK0006139biological_processnucleobase-containing compound metabolic process
KK0006364biological_processrRNA processing
KK0006396biological_processRNA processing
KK0006401biological_processRNA catabolic process
KK0008270molecular_functionzinc ion binding
KK0008408molecular_function3'-5' exonuclease activity
KK0016787molecular_functionhydrolase activity
KK0032204biological_processregulation of telomere maintenance
KK0034473biological_processU1 snRNA 3'-end processing
KK0034475biological_processU4 snRNA 3'-end processing
KK0034476biological_processU5 snRNA 3'-end processing
KK0042134molecular_functionrRNA primary transcript binding
KK0071028biological_processnuclear mRNA surveillance
KK0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
KK0071036biological_processnuclear polyadenylation-dependent snoRNA catabolic process
KK0071037biological_processnuclear polyadenylation-dependent snRNA catabolic process
KK0071038biological_processTRAMP-dependent tRNA surveillance pathway
KK0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
KK0071040biological_processnuclear polyadenylation-dependent antisense transcript catabolic process
KK0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
KK0071044biological_processhistone mRNA catabolic process
KK0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
LL0000178cellular_componentexosome (RNase complex)
LL0000460biological_processmaturation of 5.8S rRNA
LL0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
LL0000973biological_processpost-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
LL0003677molecular_functionDNA binding
LL0003690molecular_functiondouble-stranded DNA binding
LL0003723molecular_functionRNA binding
LL0003725molecular_functiondouble-stranded RNA binding
LL0005515molecular_functionprotein binding
LL0005634cellular_componentnucleus
LL0005730cellular_componentnucleolus
LL0006364biological_processrRNA processing
LL0010468biological_processregulation of gene expression
LL0030234molecular_functionenzyme regulator activity
LL0034475biological_processU4 snRNA 3'-end processing
LL0034476biological_processU5 snRNA 3'-end processing
LL0044877molecular_functionprotein-containing complex binding
LL0071028biological_processnuclear mRNA surveillance
LL0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
LL0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
LL0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
MM0000166molecular_functionnucleotide binding
MM0000292biological_processRNA fragment catabolic process
MM0000460biological_processmaturation of 5.8S rRNA
MM0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
MM0003676molecular_functionnucleic acid binding
MM0003723molecular_functionRNA binding
MM0003724molecular_functionRNA helicase activity
MM0003729molecular_functionmRNA binding
MM0003824molecular_functioncatalytic activity
MM0004386molecular_functionhelicase activity
MM0005515molecular_functionprotein binding
MM0005524molecular_functionATP binding
MM0005634cellular_componentnucleus
MM0005730cellular_componentnucleolus
MM0006364biological_processrRNA processing
MM0006397biological_processmRNA processing
MM0006401biological_processRNA catabolic process
MM0008143molecular_functionpoly(A) binding
MM0016075biological_processrRNA catabolic process
MM0016491molecular_functionoxidoreductase activity
MM0016787molecular_functionhydrolase activity
MM0016887molecular_functionATP hydrolysis activity
MM0031499cellular_componentTRAMP complex
MM0034458molecular_function3'-5' RNA helicase activity
MM0034475biological_processU4 snRNA 3'-end processing
MM0034476biological_processU5 snRNA 3'-end processing
MM0071028biological_processnuclear mRNA surveillance
MM0071031biological_processnuclear mRNA surveillance of mRNA 3'-end processing
MM0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
MM0071038biological_processTRAMP-dependent tRNA surveillance pathway
MM0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
MM0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
Functional Information from PROSITE/UniProt
site_idPS01175
Number of Residues25
DetailsRIBONUCLEASE_II Ribonuclease II family signature. HYGLavdi.YThFTSPIRRYcDvvaH
ChainResidueDetails
JJHIS831-HIS855
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues150
DetailsDomain: {"description":"S1 motif"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues67
DetailsDomain: {"description":"CSD2","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues330
DetailsDomain: {"description":"RNB","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues97
DetailsDomain: {"description":"S1 motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU00180","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues166
DetailsDomain: {"description":"3'-5' exonuclease","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16882719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2HBL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HBM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16882719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2HBM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16882719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2HBK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HBL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HBM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues156
DetailsDomain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues204
DetailsDomain: {"description":"Helicase C-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU00542","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues3
DetailsMotif: {"description":"DEVH box"}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues7
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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