2BKD

Structure of the N-terminal domain of Fragile X Mental Retardation Protein

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth N]	Agenet	e2bkdN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Agenet	ECOD (1.6)
A [auth N]	Agenet_like	e2bkdN4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Agenet_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth N]	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth N]	PF17904	FMRP KH0 domain (KH_9)	FMRP KH0 domain	This entry corresponds to the KH0 domain from the FMRP protein [1]. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein [1]. KH0 does not have the canonical G-X-X-G motif betwe ...	This entry corresponds to the KH0 domain from the FMRP protein [1]. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein [1]. KH0 does not have the canonical G-X-X-G motif between helices A and B [1]. It has been suggested that this domain may be involved in RNA binding [1].	Domain
A [auth N]	PF18336	Fragile X messenger ribonucleoprotein 1, Tudor domain (Tudor_FRX1)	Fragile X messenger ribonucleoprotein 1, Tudor domain	This is the N-terminal Tudor domain (Tud1) found in Fragile X messenger ribonucleoprotein 1 (FMR1) and its paralogues, RNA-binding proteins FXR1/2. The Tud1 domain forms a canonical Tudor barrel [1]. It is usually found in tandem with Agenet domain P ...	This is the N-terminal Tudor domain (Tud1) found in Fragile X messenger ribonucleoprotein 1 (FMR1) and its paralogues, RNA-binding proteins FXR1/2. The Tud1 domain forms a canonical Tudor barrel [1]. It is usually found in tandem with Agenet domain Pfam:PF05641.	Domain
A [auth N]	PF05641	Agenet domain (Agenet)	Agenet domain	This domain is related to the TUDOR domain Pfam:PF00567 [1]. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth N]	Fragile X messenger ribonucleoprotein 1	protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity cytoskeletal protein binding microtubule binding protein binding binding tubulin binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding regulatory RNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity N6-methyladenosine-containing RNA reader activity molecular adaptor activity cytoskeletal protein binding microtubule binding protein binding binding tubulin binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding regulatory RNA binding RNA binding siRNA binding organic cyclic compound binding nucleic acid binding signaling adaptor activity miRNA binding sequence-specific mRNA binding mRNA binding identical protein binding protein homodimerization activity protein dimerization activity poly(A) binding poly-purine tract binding single-stranded RNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding mRNA 5'-UTR binding poly(G) binding poly-pyrimidine tract binding poly(U) RNA binding mRNA 3'-UTR binding RNA strand annealing activity annealing activity translation initiation factor binding RNA stem-loop binding translation regulator activity chromatin binding protein heterodimerization activity molecular condensate scaffold activity transmembrane transporter binding G-quadruplex RNA binding translation repressor activity dynein complex binding	regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell trans-synaptic signaling regulation of biological process neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport establishment of localization negative regulation of synaptic vesicle exocytosis regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis cellular localization transport modulation of chemical synaptic transmission signaling negative regulation of regulated secretory pathway regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell negative regulation of exocytosis signal release negative regulation of cellular process regulation of signaling regulation of transport secretion regulation of neurotransmitter transport biological regulation export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication cellular process positive regulation of macromolecule biosynthetic process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process organic substance biosynthetic 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 cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process organic cyclic compound 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 catabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process 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 organic cyclic compound catabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process positive regulation of gene expression regulation of mRNA metabolic process organic substance catabolic process positive regulation of cellular biosynthetic process cellular response to stimulus cell surface receptor signaling pathway response to stimulus glutamate receptor signaling pathway signal transduction RNA splicing RNA processing developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development organonitrogen compound biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation translational initiation protein metabolic process negative regulation of protein metabolic process organonitrogen compound metabolic process regulation of translational initiation regulation of protein metabolic process negative regulation of translational initiation translation regulation of translation regulation of calcium ion transmembrane transporter activity regulation of calcium ion transport negative regulation of voltage-gated calcium channel activity negative regulation of ion transmembrane transporter activity negative regulation of calcium ion transmembrane transporter activity regulation of voltage-gated calcium channel activity calcium ion transport negative regulation of cation transmembrane transport monoatomic cation transport regulation of monoatomic ion transport inorganic ion transmembrane transport regulation of cation channel activity inorganic cation transmembrane transport transmembrane transport regulation of molecular function regulation of transmembrane transport negative regulation of calcium ion transmembrane transport negative regulation of cation channel activity monoatomic ion transmembrane transport negative regulation of monoatomic ion transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport metal ion transport negative regulation of transmembrane transport regulation of transporter activity regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport negative regulation of monoatomic ion transmembrane transport monoatomic ion transport regulation of metal ion transport regulation of monoatomic ion transmembrane transporter activity negative regulation of transporter activity negative regulation of molecular function negative regulation of calcium ion transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport RNA transport nitrogen compound transport organic substance transport nucleic acid transport mRNA transport establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport nucleocytoplasmic transport nuclear transport mRNA export from nucleus nuclear export intracellular transport RNA export from nucleus miRNA-mediated post-transcriptional gene silencing negative regulation of miRNA-mediated gene silencing post-transcriptional gene silencing negative regulation of post-transcriptional gene silencing regulation of miRNA-mediated gene silencing negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of gene silencing by regulatory ncRNA regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing regulation of mRNA processing regulation of RNA splicing RNA splicing, via transesterification reactions regulation of alternative mRNA splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile modulation by host of viral RNA genome replication biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle modulation by host of viral genome replication biological process involved in symbiotic interaction RNA biosynthetic process nucleic acid biosynthetic process modulation by host of viral process viral RNA genome replication viral process biological process involved in interaction with symbiont nucleobase-containing compound biosynthetic process viral genome replication organic cyclic compound biosynthetic process positive regulation of cell communication negative regulation of signaling negative regulation of synaptic transmission negative regulation of cell communication regulation of biological quality regulation of synaptic plasticity positive regulation of synaptic transmission negative regulation of long-term synaptic depression long-term synaptic depression regulation of long-term synaptic depression positive regulation of signaling filopodium assembly regulation of cellular component organization positive regulation of cellular component organization cell projection organization regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of filopodium assembly plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly positive regulation of viral life cycle positive regulation of viral process regulation of viral life cycle regulation of viral process intracellular transport of virus positive regulation of intracellular transport of viral material transport of virus regulation of intracellular transport of viral material positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process proteolysis organonitrogen compound catabolic process proteasomal protein catabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process regulation of protein catabolic process regulation of developmental process cellular developmental process positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development positive regulation of developmental process neurogenesis neuron differentiation dendrite development cell differentiation dendritic spine development generation of neurons neuron development DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair organelle organization stress granule assembly organelle assembly non-membrane-bounded organelle assembly negative regulation of cytoplasmic translation cytoplasmic translation regulation of cytoplasmic translation regulation of action potential system process nervous system process regulation of system process action potential transmission of nerve impulse regulation of nervous system process neuronal action potential regulation of transmission of nerve impulse regulation of multicellular organismal process regulation of neuronal action potential regulation of membrane potential regulation of mRNA stability regulation of RNA stability positive regulation of post-transcriptional gene silencing positive regulation of miRNA-mediated gene silencing positive regulation of post-transcriptional gene silencing by RNA import into cell receptor internalization regulation of receptor internalization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of receptor-mediated endocytosis positive regulation of receptor internalization positive regulation of transport endocytosis receptor-mediated endocytosis positive regulation of translation positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of phosphate metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation cellular response to virus response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle protein-containing complex ribonucleoprotein complex somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle protein-containing complex ribonucleoprotein complex messenger ribonucleoprotein complex cell projection actin-based cell projection dendritic filopodium dendrite dendritic tree filopodium neuron projection plasma membrane bounded cell projection chromosome neuron spine synapse dendritic spine postsynapse cell junction membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen cytoplasmic ribonucleoprotein granule supramolecular complex ribonucleoprotein granule axon growth cone growth cone filopodium distal axon site of polarized growth cell periphery postsynaptic membrane membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic membrane Cajal body nuclear body nucleoplasm chromocenter perinuclear region of cytoplasm dendritic spine neck cytoplasmic stress granule filopodium tip chromosome, centromeric region chromosomal region glial cell projection neuron projection cytoplasm cytoplasmic region plasma membrane bounded cell projection cytoplasm neuronal ribonucleoprotein granule postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse axon terminus neuron projection terminus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth N]	IPR047436	Fragile X messenger ribonucleoprotein 1, second Tudor-like Agenet domain	Domain
A [auth N]	IPR047440	Fragile X messenger ribonucleoprotein 1, second type I K homology domain	Domain
A [auth N]	IPR004088	K Homology domain, type 1	Domain
A [auth N]	IPR004087	K Homology domain	Domain
A [auth N]	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A [auth N]	IPR047438	Fragile X messenger ribonucleoprotein 1, first type I K homology domain	Domain
A [auth N]	IPR047431	Fragile X messenger ribonucleoprotein 1, first Tudor-like Agenet domain	Domain
A [auth N]	IPR041560	FMR1, tudor domain	Domain
A [auth N]	IPR022034	Fragile X messenger ribonucleoprotein 1-like, C-terminal core	Domain
A [auth N]	IPR040148	Fragile X messenger ribonucleoprotein 1	Family
A [auth N]	IPR032196	Fragile X messenger ribonucleoprotein 1, C-terminal region 2	Domain
A [auth N]	IPR008395	Agenet-like domain	Domain
A [auth N]	IPR040472	Synaptic functional regulator FMRP, KH0 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth N]	Pharos: Q06787	fragile X syndrome fragile X-associated tremor/ataxia syndrome primary ovarian failure gonadal dysgenesis intellectual disability Craniofacial Abnormalities autism Xq27.3q28 duplication syndrome neurodegenerative disease congenital abnormality premature ovarian failure 1 subependymal giant cell astrocytoma hydrocephalus juvenile dermatomyositis amyotrophic lateral sclerosis fragile X syndrome fragile X-associated tremor/ataxia syndrome primary ovarian failure gonadal dysgenesis intellectual disability Craniofacial Abnormalities autism Xq27.3q28 duplication syndrome neurodegenerative disease congenital abnormality premature ovarian failure 1 subependymal giant cell astrocytoma hydrocephalus juvenile dermatomyositis amyotrophic lateral sclerosis major depressive disorder atypical teratoid rhabdoid tumor bipolar disorder pancreatic intraductal papillary-mucinous neoplasm psoriasis Duchenne muscular dystrophy schizophrenia FRAXE intellectual disability large cell medulloblastoma anxiety disorder malignant glioma mixed anxiety and depressive disorder myopathy premature menopause Rett syndrome Emery-Dreifuss muscular dystrophy spina bifida gonadal agenesis hereditary ataxia lung cancer dermatomyositis sarcoidosis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.