3NTW | pdb_00003ntw

Structure of the MLLE domain of EDD in complex with a PAM2 peptide from Paip1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ntwa1	All alpha proteins	PABP domain-like	PABC (PABP) domain	PABC (PABP) domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d3ntwa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d3ntwc_	All alpha proteins	PABP domain-like	PABC (PABP) domain	PABC (PABP) domain	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PABC (PABP) domain	8068211	4003044	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PABC (PABP) domain	8068212	3000200	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	PABC (PABP) domain	8068212	3000200	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PABP	e3ntwA1	A: alpha arrays	X: PABP domain-like	H: PABC(PABP) domain (From Topology)	T: PABC(PABP) domain	F: PABP	ECOD (1.6)
C	PABP	e3ntwC1	A: alpha arrays	X: PABP domain-like	H: PABC(PABP) domain (From Topology)	T: PABC(PABP) domain	F: PABP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1900.10	Mainly Alpha	Orthogonal Bundle	c-terminal domain of poly(a) binding protein	c-terminal domain of poly(a) binding protein	CATH (4.3.0)
C	1.10.1900.10	Mainly Alpha	Orthogonal Bundle	c-terminal domain of poly(a) binding protein	c-terminal domain of poly(a) binding protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00658	MLLE domain (MLLE)	MLLE domain	The MLLE domain, also known as the PABC or CTC domain, is found at the C-terminus of cytoplasmic poly(A)-binding proteins (PABPs). It consists of a bundle of 4-5 alpha helices and contains a conserved KITGMLLE signature motif. The MLLE domain functio ...	The MLLE domain, also known as the PABC or CTC domain, is found at the C-terminus of cytoplasmic poly(A)-binding proteins (PABPs). It consists of a bundle of 4-5 alpha helices and contains a conserved KITGMLLE signature motif. The MLLE domain functions as a peptide-binding domain that interacts with PAM2 (PABP-interacting motif 2) sequences found in various PABP regulatory proteins involved in translation and mRNA decay. Key conserved residues in the MLLE domain form binding pockets that accommodate an invariant phenylalanine and other residues in the PAM2 motif. Besides PABPs, the MLLE domain is also found in the E3 ubiquitin ligase UBR5 where it serves as a protein interaction module. In some fungi, Rrm4 RNA-binding proteins contain a binding platform of 2-3 divergent MLLE domains that interact with PAM2-like motifs in the Upa1 protein to mediate attachment of mRNA-protein particles to endosomes for transport and localized translation.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	E3 ubiquitin-protein ligase UBR5	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding binding protein domain specific binding ubiquitin binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding binding protein domain specific binding ubiquitin binding ubiquitin-like protein binding RNA binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein modification-dependent macromolecule catabolic process proteolysis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein modification-dependent macromolecule catabolic process proteolysis protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins heterochromatin boundary formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process protein polyubiquitination protein branched polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process DNA repair-dependent chromatin remodeling cytoplasm protein quality control cytoplasm protein quality control by the ubiquitin-proteasome system protein K29-linked ubiquitination negative regulation of signaling signaling regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport localization import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus positive regulation of intracellular transport intracellular protein localization regulation of intracellular transport regulation of transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization establishment of protein localization to organelle positive regulation of transport protein transport regulation of cellular localization macromolecule localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport ubiquitin-dependent protein catabolic process via the N-end rule pathway regulation of protein stability regulation of biological quality DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair protein K11-linked ubiquitination protein K48-linked ubiquitination intracellular receptor signaling pathway response to lipid progesterone receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus response to hormone response to steroid hormone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway multicellular organismal process cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-17 production negative regulation of interleukin-17 production negative regulation of cytokine production regulation of interleukin-17 production negative regulation of multicellular organismal process positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway positive regulation of signaling	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex perinuclear region of cytoplasm membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, D	Polyadenylate-binding protein-interacting protein 1	translation regulator activity translation activator activity RNA binding binding nucleic acid binding	regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process negative regulation of cellular process regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process RNA destabilization nuclear-transcribed mRNA catabolic process biological regulation negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of mRNA stability positive regulation of catabolic process negative regulation of biosynthetic process positive regulation of gene expression positive regulation of mRNA catabolic process regulation of RNA stability cellular process regulation of mRNA metabolic process translation protein biosynthetic process translational initiation protein metabolic process mRNA stabilization CRD-mediated mRNA stabilization RNA stabilization positive regulation of protein metabolic process positive regulation of translation positive regulation of cytoplasmic translation regulation of protein metabolic process regulation of translation cytoplasmic translation regulation of cytoplasmic translation regulation of translational initiation biological process involved in interspecies interaction between organisms host-mediated perturbation of viral process modulation of process of another organism host-mediated activation of viral process host-mediated perturbation of symbiont process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol mCRD-mediated mRNA stability complex protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR002004	Polyadenylate-binding protein/Hyperplastic disc protein, C-terminal	Domain
A, C	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A, C	IPR024725	E3 ubiquitin-protein ligase UBR5, ubiquitin-associated domain	Domain
A, C	IPR000569	HECT domain	Domain
A, C	IPR003126	Zinc finger, UBR-type	Domain
A, C	IPR009091	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Homologous Superfamily
A, C	IPR047503	E3 ubiquitin-protein ligase UBR5, UBR-box	Domain
A, C	IPR036053	PABC (PABP) domain	Homologous Superfamily
B, D	IPR051367	mRNA Translation Regulation/Replication-dependent Histone mRNA Translation	Family
B, D	IPR016024	Armadillo-type fold	Homologous Superfamily
B, D	IPR009818	PAM2 motif	Conserved Site
B, D	IPR003890	MIF4G-like, type 3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q9H074	astrocytic tumor glioblastoma lung adenocarcinoma malignant glioma oligodendroglioma tuberculosis breast cancer interstitial cystitis lung cancer nasopharyngeal carcinoma pilocytic astrocytoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma astrocytic tumor glioblastoma lung adenocarcinoma malignant glioma oligodendroglioma tuberculosis breast cancer interstitial cystitis lung cancer nasopharyngeal carcinoma pilocytic astrocytoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma plasma cell myeloma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.