8SMO | pdb_00008smo

Crystal structure of the complex between truncated MLLE domain of PABPC1 and engineered superPAM2 peptide

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	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
B, D, F, H, J B, D, F, H, J, L, N, P	superPAM2	-	-	-
A, C, E, G, I A, C, E, G, I, K, M, O	Polyadenylate-binding protein 1	mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding translation regulator activity translation activator activity poly(A) binding poly-purine tract binding single-stranded RNA binding poly-pyrimidine tract binding poly(U) RNA binding	regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process 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 RNA catabolic process mRNA catabolic process regulation of biological process regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process 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 RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic 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 catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process nuclear-transcribed mRNA catabolic process negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 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 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biosynthetic process positive regulation of gene expression cellular process regulation of mRNA metabolic process post-transcriptional regulation of gene expression regulation of biological quality mRNA stabilization regulation of mRNA stability CRD-mediated mRNA stabilization RNA stabilization regulation of RNA stability positive regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay mRNA destabilization regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay RNA destabilization positive regulation of catabolic process positive regulation of mRNA catabolic process positive regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay regulatory ncRNA-mediated gene silencing positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process positive regulation of cytoplasmic translation protein metabolic process regulation of protein metabolic process translation regulation of translation cytoplasmic translation regulation of cytoplasmic translation positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication RNA splicing nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule membrane membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle spliceosomal complex ribonucleoprotein complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol mCRD-mediated mRNA stability complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002004	Polyadenylate-binding protein/Hyperplastic disc protein, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR006515	Polyadenylate binding protein, human types 1, 2, 3, 4	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR003954	RNA recognition motif domain, eukaryotic-type	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR000504	RNA recognition motif domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036053	PABC (PABP) domain	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR034364	PABP, RNA recognition motif 1	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR045305	PABP, RNA recognition motif 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: P11940	transitional cell carcinoma breast carcinoma urinary bladder cancer astrocytic tumor Down syndrome lung cancer Mammary Neoplasms, Human spina bifida urinary bladder neoplasm breast cancer Duchenne muscular dystrophy myopathy juvenile dermatomyositis ovarian cancer

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.