2BKD | pdb_00002bkd

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]	Piwi	e2bkdN4	A: beta barrels	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: Piwi	ECOD (v294.2)
A [auth N]	Nop10p	e2bkdN1	A: beta barrels	X: OB-fold	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Nop10p	ECOD (v294.2)

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]	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 regulatory RNA binding RNA binding siRNA binding nucleic acid binding signaling adaptor activity 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 regulatory RNA binding RNA binding siRNA 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 histone reader activity histone H3 reader activity chromatin-protein adaptor activity mRNA 3'-UTR binding RNA strand annealing activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid annealing activity macromolecular conformation isomerase activity catalytic 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 developmental process animal organ development anatomical structure development cellular response to stimulus cell surface receptor signaling pathway response to stimulus glutamate receptor signaling pathway signal transduction RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process RNA processing macromolecule metabolic process multicellular organism development multicellular organismal process nervous system development system development protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation translational initiation protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of translational initiation regulation of protein metabolic process negative regulation of metabolic process negative regulation of translational initiation regulation of macromolecule metabolic process translation regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process 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 negative regulation of monoatomic ion transport monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of voltage-gated calcium channel activity negative regulation of transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport negative regulation of monoatomic ion transmembrane transport monoatomic ion transport negative regulation of cation transmembrane transport monoatomic cation transport regulation of metal ion transport regulation of monoatomic ion transport negative regulation of transporter activity negative regulation of molecular function negative regulation of calcium ion transport transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of monoatomic cation transmembrane transport negative regulation of calcium ion transmembrane transport calcium ion transmembrane transport RNA transport nitrogen compound transport nucleic acid transport mRNA transport establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport regulation of translation at synapse, modulating synaptic transmission regulation of translation at presynapse, modulating synaptic transmission regulation of translation at presynapse regulation of translation at synapse presynaptic modulation of chemical synaptic transmission nucleocytoplasmic transport nuclear transport intercellular transport mRNA export from nucleus nuclear export intracellular transport RNA export from nucleus positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of miRNA-mediated gene silencing positive regulation of metabolic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of macromolecule metabolic process positive regulation of cellular process negative regulation of gene silencing by regulatory ncRNA regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of post-transcriptional gene silencing positive regulation of gene expression negative regulation of miRNA-mediated gene silencing post-transcriptional gene silencing negative regulation of post-transcriptional gene silencing alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of mRNA processing regulation of RNA splicing mRNA metabolic process 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 regulation of mRNA metabolic 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 biological process involved in interspecies interaction between organisms positive regulation of viral life cycle positive regulation of viral process viral life cycle biological process involved in symbiotic interaction regulation of viral life cycle regulation of viral process intracellular transport of virus viral process positive regulation of intracellular transport of viral material transport of virus regulation of intracellular transport of viral material regulation of biological process involved in symbiotic interaction organelle organization organelle assembly membraneless organelle assembly host-mediated perturbation of viral process host-mediated perturbation of viral RNA genome replication host-mediated perturbation of symbiont process viral genome replication viral RNA genome replication modulation of process of another organism positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process macromolecule catabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process 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 stress granule 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 catabolic process RNA catabolic process mRNA catabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of RNA stability nucleic acid catabolic process 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 nervous system development regulation of long-term neuronal synaptic plasticity regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of cell differentiation positive regulation of long-term neuronal synaptic plasticity positive regulation of neurogenesis regulation of neuronal synaptic plasticity regulation of multicellular organismal development positive regulation of cell development positive regulation of multicellular organismal process 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 cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol cell projection actin-based cell projection dendritic filopodium dendrite dendritic tree filopodium somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol cell projection actin-based cell projection dendritic filopodium dendrite dendritic tree filopodium neuron projection plasma membrane bounded cell projection intracellular organelle organelle membraneless organelle intracellular membraneless organelle 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 protein-containing complex ribonucleoprotein complex cell periphery postsynaptic membrane membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic membrane Cajal body nuclear body nucleoplasm nuclear ribonucleoprotein granule chromocenter perinuclear region of cytoplasm cytoplasmic stress granule filopodium tip chromosome, centromeric region chromosomal region glial cell projection neuron 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]	: 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 Duchenne muscular dystrophy psoriasis schizophrenia FRAXE intellectual disability large cell medulloblastoma anxiety disorder malignant glioma mixed anxiety and depressive disorder myopathy premature menopause Emery-Dreifuss muscular dystrophy Rett syndrome spina bifida gonadal agenesis hereditary ataxia lung cancer dermatomyositis sarcoidosis

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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.