6R5K | pdb_00006r5k

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


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AANAPC4_WD40_6e6r5kA3 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: ANAPC4_WD40_6ECOD (1.6)
AUCHe6r5kA1 A: a+b complex topologyX: Cysteine proteinases-likeH: Cysteine proteinases (From Topology)T: Cysteine proteinasesF: UCHECOD (1.6)
ARNase_Te6r5kA2 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: RNase_TECOD (1.6)
E [auth H]RRM_1_1e6r5kH2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_1ECOD (1.6)
E [auth H]RRM_1e6r5kH4 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1ECOD (1.6)
E [auth H]RRM_1_5e6r5kH1 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_5ECOD (1.6)
E [auth H]RRM_1_7e6r5kH3 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_7ECOD (1.6)
D [auth F]RRM_1e6r5kF2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1ECOD (1.6)
D [auth F]RRM_1_7e6r5kF1 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_7ECOD (1.6)
B [auth D]RRM_1_1e6r5kD2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_1ECOD (1.6)
B [auth D]RRM_1e6r5kD4 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1ECOD (1.6)
B [auth D]RRM_1_5e6r5kD1 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_5ECOD (1.6)
B [auth D]RRM_1_7e6r5kD3 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: RRM_1_7ECOD (1.6)
G [auth O]F_UNCLASSIFIEDe6r5kO1 A: alpha arraysX: Dimerization domain in caprin-1 and PAN3 (From Topology)H: Dimerization domain in caprin-1 and PAN3 (From Topology)T: Dimerization domain in caprin-1 and PAN3F: F_UNCLASSIFIEDECOD (1.6)
G [auth O]Pkinase_Tyre6r5kO2 A: a+b complex topologyX: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)H: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: Pkinase_TyrECOD (1.6)
F [auth N]F_UNCLASSIFIEDe6r5kN2 A: alpha arraysX: Dimerization domain in caprin-1 and PAN3 (From Topology)H: Dimerization domain in caprin-1 and PAN3 (From Topology)T: Dimerization domain in caprin-1 and PAN3F: F_UNCLASSIFIEDECOD (1.6)
F [auth N]Pkinase_Tyre6r5kN1 A: a+b complex topologyX: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)H: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: Pkinase_TyrECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00929Exonuclease (RNase_T)ExonucleaseThis family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; Domain
PF13423Ubiquitin carboxyl-terminal hydrolase (UCH_1)Ubiquitin carboxyl-terminal hydrolaseThis is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 an ...This is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 and PAN3), involved in the initial trimming of poly(A) tails [1-3].
Domain
B [auth D],
D [auth F],
E [auth H]
PF00076RNA recognition motif (RRM_1)RNA recognition motifThe RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Domain
G [auth O]PF18101Pan3 C-terminal knob domain (Pan3_CK)Pan3 C-terminal knob domainThis entry represents the Pan3 C-terminal knob domain. Domain
F [auth N]PF18101Pan3 C-terminal knob domain (Pan3_CK)Pan3 C-terminal knob domainThis entry represents the Pan3 C-terminal knob domain. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
PAN2-PAN3 deadenylation complex catalytic subunit PAN2
B [auth D],
D [auth F],
E [auth H]
Polyadenylate-binding protein, cytoplasmic and nuclear
G [auth O]PAN2-PAN3 deadenylation complex subunit PAN3
F [auth N]PAN2-PAN3 deadenylation complex subunit PAN3
C [auth E]poly(A) RNA---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR036397Ribonuclease H superfamilyHomologous Superfamily
IPR030843PAN2-PAN3 deadenylation complex catalytic subunit PAN2Family
IPR028881PAN2, UCH domainDomain
IPR028889Ubiquitin specific protease UPS, catalytic domainDomain
IPR048841PAN2-PAN3 deadenylation complex catalytic subunit PAN2, N-terminalDomain
IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
IPR013520Ribonuclease H-like domainDomain
IPR038765Papain-like cysteine peptidase superfamilyHomologous Superfamily
IPR050785PAN2-PAN3 complex catalytic subunitFamily
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
B [auth D],
D [auth F],
E [auth H]
IPR002004Polyadenylate-binding protein/Hyperplastic disc protein, C-terminalDomain
B [auth D],
D [auth F],
E [auth H]
IPR006515Polyadenylate binding protein, human types 1, 2, 3, 4Family
B [auth D],
D [auth F],
E [auth H]
IPR003954RNA recognition motif domain, eukaryotic-typeDomain
B [auth D],
D [auth F],
E [auth H]
IPR000504RNA recognition motif domainDomain
B [auth D],
D [auth F],
E [auth H]
IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
B [auth D],
D [auth F],
E [auth H]
IPR036053PABC (PABP) domainHomologous Superfamily
B [auth D],
D [auth F],
E [auth H]
IPR034364PABP, RNA recognition motif 1Domain
B [auth D],
D [auth F],
E [auth H]
IPR035979RNA-binding domain superfamilyHomologous Superfamily
B [auth D],
D [auth F],
E [auth H]
IPR045305PABP, RNA recognition motif 2Domain
G [auth O]IPR030844PAN2-PAN3 deadenylation complex subunit PAN3Family
G [auth O]IPR000571Zinc finger, CCCH-typeDomain
G [auth O]IPR011009Protein kinase-like domain superfamilyHomologous Superfamily
G [auth O]IPR000719Protein kinase domainDomain
G [auth O]IPR041332Pan3, C-terminal knob domainDomain
F [auth N]IPR030844PAN2-PAN3 deadenylation complex subunit PAN3Family
F [auth N]IPR000571Zinc finger, CCCH-typeDomain
F [auth N]IPR011009Protein kinase-like domain superfamilyHomologous Superfamily
F [auth N]IPR000719Protein kinase domainDomain
F [auth N]IPR041332Pan3, C-terminal knob domainDomain