5KL1 | pdb_00005kl1

Crystal structure of the Pumilio-Nos-hunchback RNA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Nanos zinc-finger domain	8047531	4005681	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Retroviral zinc finger-like domains	8054186	3001193	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8085029	3000116	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)
B	zf-nanos	e5kl1B1	A: few secondary structure elements	X: zinc-finger domain of Nanos (From Topology)	H: zinc-finger domain of Nanos (From Topology)	T: zinc-finger domain of Nanos	F: zf-nanos	ECOD (1.6)
A	PUF	e5kl1A1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PUF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	4.10.60.30	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Nanos, RNA-binding domain	CATH (4.3.0)
A	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF05741	Nanos RNA binding domain (zf-nanos)	Nanos RNA binding domain	-	Family
A	PF00806	Pumilio-family RNA binding repeat (PUF)	Pumilio-family RNA binding repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	RNA (5'-R(APAPAPUPUPGPUPAPCPAPUPA)-3')	-	-	-
B	Protein nanos	RNA binding binding nucleic acid binding mRNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation 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 developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation 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 developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation cell differentiation anatomical structure development germ cell development multicellular organism development multicellular organismal process segmentation pattern specification process regionalization germ cell migration cell migration cell motility germ-line stem cell population maintenance maintenance of cell number stem cell population maintenance negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death blastoderm segmentation embryonic pattern specification anterior/posterior axis specification, embryo anterior/posterior pattern specification embryo development tripartite regional subdivision embryonic axis specification anterior/posterior axis specification axis specification cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cellular component organization or biogenesis system development plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development oocyte development cell maturation oocyte axis specification oocyte construction oocyte anterior/posterior axis specification developmental maturation anatomical structure maturation maternal determination of anterior/posterior axis, embryo oocyte differentiation regulation of growth developmental growth cellular component biogenesis cellular component assembly negative regulation of cell junction assembly neuromuscular junction development negative regulation of growth regulation of synaptic assembly at neuromuscular junction regulation of synapse structure or activity synapse organization regulation of biological quality regulation of neuromuscular junction development negative regulation of cellular component organization negative regulation of synaptic assembly at neuromuscular junction regulation of cell junction assembly negative regulation of developmental growth synapse assembly negative regulation of multicellular organismal process regulation of cellular component organization regulation of developmental process regulation of nervous system development cell junction assembly negative regulation of nervous system development regulation of multicellular organismal process regulation of synapse assembly negative regulation of neuromuscular junction development regulation of multicellular organismal development regulation of developmental growth negative regulation of developmental process growth negative regulation of synapse organization regulation of cellular component biogenesis regulation of synapse organization cell junction organization synaptic assembly at neuromuscular junction negative regulation of synapse assembly	cellular anatomical structure neuromuscular junction synapse cell junction postsynapse postsynapse of neuromuscular junction neuron projection cytoplasm intracellular anatomical structure cytoplasmic ribonucleoprotein granule neuron projection intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cellular anatomical structure neuromuscular junction synapse cell junction postsynapse postsynapse of neuromuscular junction neuron projection cytoplasm intracellular anatomical structure cytoplasmic ribonucleoprotein granule neuron projection intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection ribonucleoprotein granule intracellular organelle cell projection organelle neuronal ribonucleoprotein granule membraneless organelle cytoplasm supramolecular complex perinuclear region of cytoplasm pole plasm
A	Maternal protein pumilio	mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity sequence-specific mRNA binding protein-containing complex binding CCR4-NOT complex binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cell cycle mitotic cell cycle protein biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation negative regulation of gene expression regulation of translation developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation cell differentiation anatomical structure development germ cell development germ cell migration cell migration cell motility post-transcriptional gene silencing multicellular organismal process blastoderm segmentation embryonic pattern specification anterior/posterior axis specification, embryo anterior/posterior pattern specification segmentation pattern specification process embryo development regionalization tripartite regional subdivision embryonic axis specification multicellular organism development anterior/posterior axis specification axis specification positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay nucleobase-containing compound catabolic process positive regulation of RNA metabolic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of cellular process RNA destabilization nuclear-transcribed mRNA catabolic process regulation of catabolic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process negative regulation of cell cycle regulation of cell cycle positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay RNA decapping deadenylation-independent decapping of nuclear-transcribed mRNA mRNA methylguanosine-cap decapping regulation of deadenylation-independent decapping of nuclear-transcribed mRNA cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of ERBB signaling pathway regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cellular component organization or biogenesis system development plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development behavior adult behavior response to alcohol response to chemical behavioral response to ethanol response to oxygen-containing compound response to ethanol 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 system process learning or memory long-term memory nervous system process cognition memory positive regulation of protein metabolic process positive regulation of translation positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of gene expression trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling head involution embryo development ending in birth or egg hatching embryonic morphogenesis embryonic development via the syncytial blastoderm regulation of growth regulation of cellular component organization regulation of developmental process developmental growth cellular component biogenesis cellular component assembly neuromuscular junction development cell junction assembly regulation of synaptic assembly at neuromuscular junction regulation of synapse structure or activity synapse organization regulation of synapse assembly regulation of neuromuscular junction development regulation of developmental growth growth regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synaptic assembly at neuromuscular junction synapse assembly	axon synapse type Ib terminal bouton neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection cellular anatomical structure distal axon terminal bouton cell junction neuron projection terminus type I terminal bouton axon synapse type Ib terminal bouton neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection cellular anatomical structure distal axon terminal bouton cell junction neuron projection terminus type I terminal bouton membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system type Is terminal bouton cytoplasm neuromuscular junction neuron projection cytoplasm cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm ribonucleoprotein granule neuronal ribonucleoprotein granule membraneless organelle supramolecular complex muscle cell postsynaptic specialization postsynapse postsynaptic specialization postsynapse of neuromuscular junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR008705	Nanos/Xcat2	Family
B	IPR038129	Nanos domain superfamily	Homologous Superfamily
B	IPR024161	Zinc finger, nanos-type	Domain
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR001313	Pumilio RNA-binding repeat	Repeat
A	IPR033712	Pumilio, RNA binding domain	Domain
A	IPR033133	Pumilio homology domain	Domain

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.