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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6R5K

Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase

Functional Information from GO Data
ChainGOidnamespacecontents
A0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
A0000289biological_processnuclear-transcribed mRNA poly(A) tail shortening
A0000932cellular_componentP-body
A0003676molecular_functionnucleic acid binding
A0004518molecular_functionnuclease activity
A0004527molecular_functionexonuclease activity
A0004535molecular_functionpoly(A)-specific ribonuclease activity
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0006301biological_processDNA damage tolerance
A0006397biological_processmRNA processing
A0008270molecular_functionzinc ion binding
A0016787molecular_functionhydrolase activity
A0031251cellular_componentPAN complex
A0046872molecular_functionmetal ion binding
D0003676molecular_functionnucleic acid binding
D0003723molecular_functionRNA binding
D0003729molecular_functionmRNA binding
D0003730molecular_functionmRNA 3'-UTR binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0005840cellular_componentribosome
D0006397biological_processmRNA processing
D0006417biological_processregulation of translation
D0006446biological_processregulation of translational initiation
D0008143molecular_functionpoly(A) binding
D0008266molecular_functionpoly(U) RNA binding
D0008428molecular_functionribonuclease inhibitor activity
D0010494cellular_componentcytoplasmic stress granule
D0031124biological_processmRNA 3'-end processing
D0051028biological_processmRNA transport
D0060211biological_processregulation of nuclear-transcribed mRNA poly(A) tail shortening
D0140693molecular_functionmolecular condensate scaffold activity
D1990841molecular_functionpromoter-specific chromatin binding
D1990904cellular_componentribonucleoprotein complex
F0003676molecular_functionnucleic acid binding
F0003723molecular_functionRNA binding
F0003729molecular_functionmRNA binding
F0003730molecular_functionmRNA 3'-UTR binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0005840cellular_componentribosome
F0006397biological_processmRNA processing
F0006417biological_processregulation of translation
F0006446biological_processregulation of translational initiation
F0008143molecular_functionpoly(A) binding
F0008266molecular_functionpoly(U) RNA binding
F0008428molecular_functionribonuclease inhibitor activity
F0010494cellular_componentcytoplasmic stress granule
F0031124biological_processmRNA 3'-end processing
F0051028biological_processmRNA transport
F0060211biological_processregulation of nuclear-transcribed mRNA poly(A) tail shortening
F0140693molecular_functionmolecular condensate scaffold activity
F1990841molecular_functionpromoter-specific chromatin binding
F1990904cellular_componentribonucleoprotein complex
H0003676molecular_functionnucleic acid binding
H0003723molecular_functionRNA binding
H0003729molecular_functionmRNA binding
H0003730molecular_functionmRNA 3'-UTR binding
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0005840cellular_componentribosome
H0006397biological_processmRNA processing
H0006417biological_processregulation of translation
H0006446biological_processregulation of translational initiation
H0008143molecular_functionpoly(A) binding
H0008266molecular_functionpoly(U) RNA binding
H0008428molecular_functionribonuclease inhibitor activity
H0010494cellular_componentcytoplasmic stress granule
H0031124biological_processmRNA 3'-end processing
H0051028biological_processmRNA transport
H0060211biological_processregulation of nuclear-transcribed mRNA poly(A) tail shortening
H0140693molecular_functionmolecular condensate scaffold activity
H1990841molecular_functionpromoter-specific chromatin binding
H1990904cellular_componentribonucleoprotein complex
N0000289biological_processnuclear-transcribed mRNA poly(A) tail shortening
N0003723molecular_functionRNA binding
N0004672molecular_functionprotein kinase activity
N0005524molecular_functionATP binding
N0006468biological_processprotein phosphorylation
N0031251cellular_componentPAN complex
O0000166molecular_functionnucleotide binding
O0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
O0000289biological_processnuclear-transcribed mRNA poly(A) tail shortening
O0000932cellular_componentP-body
O0003723molecular_functionRNA binding
O0004672molecular_functionprotein kinase activity
O0005515molecular_functionprotein binding
O0005524molecular_functionATP binding
O0005737cellular_componentcytoplasm
O0006281biological_processDNA repair
O0006301biological_processDNA damage tolerance
O0006397biological_processmRNA processing
O0006468biological_processprotein phosphorylation
O0008143molecular_functionpoly(A) binding
O0008270molecular_functionzinc ion binding
O0031251cellular_componentPAN complex
O0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues5
Detailsbinding site for residue MG E 101
ChainResidue
AHIS1015
ALEU1047
EA65
EA66
EMG102
site_idAC2
Number of Residues5
Detailsbinding site for residue MG E 102
ChainResidue
EMG101
AHIS1015
ALEU1047
ASER1048
EA65
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues41
DetailsRepeat: {"description":"WD 2","evidences":[{"source":"HAMAP-Rule","id":"MF_03182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues39
DetailsRepeat: {"description":"WD 3","evidences":[{"source":"HAMAP-Rule","id":"MF_03182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues39
DetailsRepeat: {"description":"WD 4","evidences":[{"source":"HAMAP-Rule","id":"MF_03182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues39
DetailsRepeat: {"description":"WD 5","evidences":[{"source":"HAMAP-Rule","id":"MF_03182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"24880344","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4Q8G","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"O95453","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_03182","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24880344","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"O95453","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_03182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues234
DetailsDomain: {"description":"RRM 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00176","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues154
DetailsDomain: {"description":"RRM 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00176","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues154
DetailsDomain: {"description":"RRM 3","evidences":[{"source":"PROSITE-ProRule","id":"PRU00176","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues154
DetailsDomain: {"description":"RRM 4","evidences":[{"source":"PROSITE-ProRule","id":"PRU00176","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues72
DetailsRegion: {"description":"Required and sufficient for nuclear import","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues3
DetailsModified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"23865587","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues182
DetailsRegion: {"description":"Knob domain","evidences":[{"source":"HAMAP-Rule","id":"MF_03181","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24880344","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues76
DetailsCoiled coil: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03181","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24880344","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03181","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

249697

PDB entries from 2026-02-25

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