Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

5C0W

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

Functional Information from GO Data
ChainGOidnamespacecontents
A0000176cellular_componentnuclear exosome (RNase complex)
A0000177cellular_componentcytoplasmic exosome (RNase complex)
A0000178cellular_componentexosome (RNase complex)
A0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
A0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
A0000956biological_processnuclear-transcribed mRNA catabolic process
A0003674molecular_functionmolecular_function
A0003723molecular_functionRNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0006364biological_processrRNA processing
A0006396biological_processRNA processing
A0006401biological_processRNA catabolic process
A0016075biological_processrRNA catabolic process
A0034473biological_processU1 snRNA 3'-end processing
A0034475biological_processU4 snRNA 3'-end processing
A0034476biological_processU5 snRNA 3'-end processing
A0035925molecular_functionmRNA 3'-UTR AU-rich region binding
A0071028biological_processnuclear mRNA surveillance
A0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
A0071038biological_processTRAMP-dependent tRNA surveillance pathway
B0000176cellular_componentnuclear exosome (RNase complex)
B0000177cellular_componentcytoplasmic exosome (RNase complex)
B0000178cellular_componentexosome (RNase complex)
B0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
B0000956biological_processnuclear-transcribed mRNA catabolic process
B0003674molecular_functionmolecular_function
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005730cellular_componentnucleolus
B0005737cellular_componentcytoplasm
B0006364biological_processrRNA processing
B0006396biological_processRNA processing
B0006401biological_processRNA catabolic process
B0016075biological_processrRNA catabolic process
B0034473biological_processU1 snRNA 3'-end processing
B0034475biological_processU4 snRNA 3'-end processing
B0034476biological_processU5 snRNA 3'-end processing
B0070478biological_processnuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
B0071028biological_processnuclear mRNA surveillance
B0071038biological_processTRAMP-dependent tRNA surveillance pathway
B0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
B0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
C0000176cellular_componentnuclear exosome (RNase complex)
C0000177cellular_componentcytoplasmic exosome (RNase complex)
C0000178cellular_componentexosome (RNase complex)
C0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
C0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C0000956biological_processnuclear-transcribed mRNA catabolic process
C0003674molecular_functionmolecular_function
C0003723molecular_functionRNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005730cellular_componentnucleolus
C0005737cellular_componentcytoplasm
C0006364biological_processrRNA processing
C0006396biological_processRNA processing
C0006397biological_processmRNA processing
C0006401biological_processRNA catabolic process
C0006402biological_processmRNA catabolic process
C0016072biological_processrRNA metabolic process
C0016075biological_processrRNA catabolic process
C0034473biological_processU1 snRNA 3'-end processing
C0034475biological_processU4 snRNA 3'-end processing
C0034476biological_processU5 snRNA 3'-end processing
C0035925molecular_functionmRNA 3'-UTR AU-rich region binding
C0071028biological_processnuclear mRNA surveillance
C0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
C0071038biological_processTRAMP-dependent tRNA surveillance pathway
C0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
D0000176cellular_componentnuclear exosome (RNase complex)
D0000177cellular_componentcytoplasmic exosome (RNase complex)
D0000178cellular_componentexosome (RNase complex)
D0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
D0000956biological_processnuclear-transcribed mRNA catabolic process
D0003674molecular_functionmolecular_function
D0003723molecular_functionRNA binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005730cellular_componentnucleolus
D0005737cellular_componentcytoplasm
D0006364biological_processrRNA processing
D0006396biological_processRNA processing
D0006401biological_processRNA catabolic process
D0016075biological_processrRNA catabolic process
D0034475biological_processU4 snRNA 3'-end processing
D0071028biological_processnuclear mRNA surveillance
D0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
D0071038biological_processTRAMP-dependent tRNA surveillance pathway
D0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
D0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
E0000176cellular_componentnuclear exosome (RNase complex)
E0000177cellular_componentcytoplasmic exosome (RNase complex)
E0000178cellular_componentexosome (RNase complex)
E0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
E0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
E0000956biological_processnuclear-transcribed mRNA catabolic process
E0003674molecular_functionmolecular_function
E0003723molecular_functionRNA binding
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005730cellular_componentnucleolus
E0005737cellular_componentcytoplasm
E0006364biological_processrRNA processing
E0006396biological_processRNA processing
E0006401biological_processRNA catabolic process
E0016075biological_processrRNA catabolic process
E0034473biological_processU1 snRNA 3'-end processing
E0034475biological_processU4 snRNA 3'-end processing
E0034476biological_processU5 snRNA 3'-end processing
E0035925molecular_functionmRNA 3'-UTR AU-rich region binding
E0071028biological_processnuclear mRNA surveillance
E0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
E0071038biological_processTRAMP-dependent tRNA surveillance pathway
F0000176cellular_componentnuclear exosome (RNase complex)
F0000177cellular_componentcytoplasmic exosome (RNase complex)
F0000178cellular_componentexosome (RNase complex)
F0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
F0000956biological_processnuclear-transcribed mRNA catabolic process
F0003674molecular_functionmolecular_function
F0003723molecular_functionRNA binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005730cellular_componentnucleolus
F0005737cellular_componentcytoplasm
F0006364biological_processrRNA processing
F0006396biological_processRNA processing
F0006401biological_processRNA catabolic process
F0016075biological_processrRNA catabolic process
F0034475biological_processU4 snRNA 3'-end processing
F0071028biological_processnuclear mRNA surveillance
F0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
F0071038biological_processTRAMP-dependent tRNA surveillance pathway
F0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
F0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
G0000176cellular_componentnuclear exosome (RNase complex)
G0000177cellular_componentcytoplasmic exosome (RNase complex)
G0000178cellular_componentexosome (RNase complex)
G0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
G0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
G0000956biological_processnuclear-transcribed mRNA catabolic process
G0003723molecular_functionRNA binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005730cellular_componentnucleolus
G0005737cellular_componentcytoplasm
G0006364biological_processrRNA processing
G0006396biological_processRNA processing
G0006401biological_processRNA catabolic process
G0030145molecular_functionmanganese ion binding
G0034475biological_processU4 snRNA 3'-end processing
G0043229cellular_componentintracellular organelle
G0071034biological_processCUT catabolic process
G0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
G0071038biological_processTRAMP-dependent tRNA surveillance pathway
G0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
H0000176cellular_componentnuclear exosome (RNase complex)
H0000177cellular_componentcytoplasmic exosome (RNase complex)
H0000178cellular_componentexosome (RNase complex)
H0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
H0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
H0000956biological_processnuclear-transcribed mRNA catabolic process
H0003674molecular_functionmolecular_function
H0003723molecular_functionRNA binding
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005730cellular_componentnucleolus
H0005737cellular_componentcytoplasm
H0006364biological_processrRNA processing
H0006396biological_processRNA processing
H0006401biological_processRNA catabolic process
H0034475biological_processU4 snRNA 3'-end processing
H0071028biological_processnuclear mRNA surveillance
H0071034biological_processCUT catabolic process
H0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
H0071038biological_processTRAMP-dependent tRNA surveillance pathway
H0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
I0000176cellular_componentnuclear exosome (RNase complex)
I0000177cellular_componentcytoplasmic exosome (RNase complex)
I0000178cellular_componentexosome (RNase complex)
I0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
I0000956biological_processnuclear-transcribed mRNA catabolic process
I0003674molecular_functionmolecular_function
I0003723molecular_functionRNA binding
I0005515molecular_functionprotein binding
I0005634cellular_componentnucleus
I0005730cellular_componentnucleolus
I0005737cellular_componentcytoplasm
I0006364biological_processrRNA processing
I0006396biological_processRNA processing
I0006397biological_processmRNA processing
I0006401biological_processRNA catabolic process
I0070481biological_processnuclear-transcribed mRNA catabolic process, non-stop decay
I0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
I0071038biological_processTRAMP-dependent tRNA surveillance pathway
J0000049molecular_functiontRNA binding
J0000175molecular_function3'-5'-RNA exonuclease activity
J0000176cellular_componentnuclear exosome (RNase complex)
J0000177cellular_componentcytoplasmic exosome (RNase complex)
J0000178cellular_componentexosome (RNase complex)
J0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
J0003676molecular_functionnucleic acid binding
J0003723molecular_functionRNA binding
J0004519molecular_functionendonuclease activity
J0004521molecular_functionRNA endonuclease activity
J0004527molecular_functionexonuclease activity
J0004540molecular_functionRNA nuclease activity
J0005515molecular_functionprotein binding
J0005634cellular_componentnucleus
J0005730cellular_componentnucleolus
J0005737cellular_componentcytoplasm
J0005739cellular_componentmitochondrion
J0006364biological_processrRNA processing
J0006396biological_processRNA processing
J0006397biological_processmRNA processing
J0006401biological_processRNA catabolic process
J0016075biological_processrRNA catabolic process
J0043628biological_processregulatory ncRNA 3'-end processing
J0070651biological_processnonfunctional rRNA decay
J0071028biological_processnuclear mRNA surveillance
J0071031biological_processnuclear mRNA surveillance of mRNA 3'-end processing
J0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
J0071038biological_processTRAMP-dependent tRNA surveillance pathway
J0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
K0000166molecular_functionnucleotide binding
K0000175molecular_function3'-5'-RNA exonuclease activity
K0000176cellular_componentnuclear exosome (RNase complex)
K0000178cellular_componentexosome (RNase complex)
K0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
K0000973biological_processpost-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
K0003676molecular_functionnucleic acid binding
K0003723molecular_functionRNA binding
K0003727molecular_functionsingle-stranded RNA binding
K0004527molecular_functionexonuclease activity
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0005730cellular_componentnucleolus
K0006139biological_processnucleobase-containing compound metabolic process
K0006364biological_processrRNA processing
K0006396biological_processRNA processing
K0006401biological_processRNA catabolic process
K0008270molecular_functionzinc ion binding
K0008408molecular_function3'-5' exonuclease activity
K0032204biological_processregulation of telomere maintenance
K0034473biological_processU1 snRNA 3'-end processing
K0034475biological_processU4 snRNA 3'-end processing
K0034476biological_processU5 snRNA 3'-end processing
K0042134molecular_functionrRNA primary transcript binding
K0044237biological_processcellular metabolic process
K0071028biological_processnuclear mRNA surveillance
K0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
K0071036biological_processnuclear polyadenylation-dependent snoRNA catabolic process
K0071037biological_processnuclear polyadenylation-dependent snRNA catabolic process
K0071038biological_processTRAMP-dependent tRNA surveillance pathway
K0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
K0071040biological_processnuclear polyadenylation-dependent antisense transcript catabolic process
K0071042biological_processnuclear polyadenylation-dependent mRNA catabolic process
K0071044biological_processhistone mRNA catabolic process
K0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
L0000178cellular_componentexosome (RNase complex)
L0000460biological_processmaturation of 5.8S rRNA
L0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
L0000973biological_processpost-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
L0003677molecular_functionDNA binding
L0003690molecular_functiondouble-stranded DNA binding
L0003723molecular_functionRNA binding
L0003725molecular_functiondouble-stranded RNA binding
L0005634cellular_componentnucleus
L0005730cellular_componentnucleolus
L0006364biological_processrRNA processing
L0010468biological_processregulation of gene expression
L0030234molecular_functionenzyme regulator activity
L0034475biological_processU4 snRNA 3'-end processing
L0034476biological_processU5 snRNA 3'-end processing
L0044877molecular_functionprotein-containing complex binding
L0071028biological_processnuclear mRNA surveillance
L0071035biological_processnuclear polyadenylation-dependent rRNA catabolic process
L0071039biological_processnuclear polyadenylation-dependent CUT catabolic process
L0071051biological_processpoly(A)-dependent snoRNA 3'-end processing
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue MG J 1101
ChainResidue
JASP543
JASP552
RA-1
RA-2

site_idAC2
Number of Residues4
Detailsbinding site for residue ZN J 1102
ChainResidue
JCYS47
JCYS52
JCYS55
JHIS184

Functional Information from PROSITE/UniProt
site_idPS01175
Number of Residues25
DetailsRIBONUCLEASE_II Ribonuclease II family signature. HYGLavdi.YThFTSPIRRYcDvvaH
ChainResidueDetails
JHIS831-HIS855

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:16882719, ECO:0007744|PDB:2HBL, ECO:0007744|PDB:2HBM
ChainResidueDetails
KGLU240
KASP365
KASP238

site_idSWS_FT_FI2
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:16882719, ECO:0007744|PDB:2HBM
ChainResidueDetails
KTRP299
KLYS342
KGLN345
KHIS241

site_idSWS_FT_FI3
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|PubMed:16882719, ECO:0007744|PDB:2HBK, ECO:0007744|PDB:2HBL, ECO:0007744|PDB:2HBM
ChainResidueDetails
KASN296

site_idSWS_FT_FI4
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950
ChainResidueDetails
KSER138

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18407956
ChainResidueDetails
KTHR520

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:19779198
ChainResidueDetails
KSER640

site_idSWS_FT_FI7
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198
ChainResidueDetails
KSER645

220472

PDB entries from 2024-05-29

PDB statisticsPDBj update infoContact PDBjnumon