6F9W | pdb_00006f9w

Crystal structure of the LSM domain of LSM14 in complex with a C-terminal peptide of 4E-T

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	d6f9wa_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	LSM14 N-terminal domain-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	LSM14 N-terminal domain-like	8086789	4001796	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sm-like ribonucleoproteins	8086790	3000419	SCOP2 (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	LSM14	e6f9wA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM14	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12701	Scd6-like Sm domain (LSM14)	Scd6-like Sm domain	The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans [1]. The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it ...	The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans [1]. The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain [1,2]. In addition both EDC3 and Scd6p are found fused to the FDF domain [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Eukaryotic translation initiation factor 4E transporter	protein binding binding kinase binding enzyme binding RNA binding nucleic acid binding mRNA binding nucleocytoplasmic carrier activity nuclear export signal receptor activity molecular carrier activity	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process maintenance of cell number stem cell population maintenance miRNA-mediated gene silencing by inhibition of translation regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing post-transcriptional gene silencing positive regulation of macromolecule biosynthetic 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 regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process nucleic acid catabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA negative regulation of RNA metabolic process RNA decapping 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 positive regulation of cellular process mRNA methylguanosine-cap decapping negative regulation of catabolic process nuclear-transcribed mRNA catabolic process RNA destabilization negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA positive regulation of gene expression positive regulation of mRNA catabolic process regulation of RNA stability regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA regulation of mRNA metabolic process cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly membraneless organelle assembly cellular component organization or biogenesis establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport mRNA stabilization RNA stabilization 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	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol cytoplasmic ribonucleoprotein granule P-body PML body
A	Protein LSM14 homolog A	RNA binding double-stranded RNA binding binding nucleic acid binding single-stranded RNA binding mRNA binding DNA binding double-stranded DNA binding	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular response to stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to stimulus response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus RIG-I signaling pathway regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response defense response to symbiont immune system process cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly membraneless organelle assembly cellular component organization or biogenesis positive regulation of cell communication positive regulation of signal transduction regulation of type I interferon-mediated signaling pathway response to cytokine regulation of signal transduction interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of response to cytokine stimulus response to chemical response to type I interferon positive regulation of type I interferon-mediated signaling pathway positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway response to peptide type I interferon-mediated signaling pathway regulation of cell communication positive regulation of cytokine-mediated signaling pathway positive regulation of signaling stress granule assembly microtubule cytoskeleton organization mitotic cell cycle mitotic sister chromatid segregation cell cycle chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation spindle assembly mitotic spindle organization mitotic spindle assembly nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization defense response to virus response to virus	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol mitotic spindle cytoskeleton intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol mitotic spindle cytoskeleton spindle microtubule cytoskeleton P-body protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR018862	Eukaryotic translation initiation factor 4E binding protein	Family
A	IPR025762	DFDF domain	Domain
A	IPR019050	FDF domain	Domain
A	IPR025761	FFD box	Domain
A	IPR047575	Sm domain	Domain
A	IPR010920	LSM domain superfamily	Homologous Superfamily
A	IPR025609	Lsm14-like, N-terminal	Domain
A	IPR025768	TFG box	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9NRA8	atypical teratoid rhabdoid tumor lung cancer ovarian cancer dermatomyositis myopathy subependymal giant cell astrocytoma glioblastoma osteosarcoma
A	Pharos: Q8ND56	amyotrophic lateral sclerosis lymphoplasmacytic lymphoma osteosarcoma psoriasis atypical teratoid rhabdoid tumor malignant ependymoma ovarian cancer dermatomyositis medulloblastoma 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.