3TRZ | pdb_00003trz

Mouse Lin28A in complex with let-7d microRNA pre-element

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	CSD	e3trzF4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: CSD	ECOD (1.6)
F	zf-CCHC	e3trzF3	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
F	zf-CCHC_2_like_1	e3trzF2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC_2_like_1	ECOD (1.6)
E	CSD	e3trzE4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: CSD	ECOD (1.6)
E	zf-CCHC	e3trzE3	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
E	zf-CCHC_2_like_1	e3trzE2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC_2_like_1	ECOD (1.6)
D	CSD	e3trzD4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: CSD	ECOD (1.6)
D	zf-CCHC	e3trzD3	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
D	zf-CCHC_2_like_1	e3trzD2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC_2_like_1	ECOD (1.6)
C	CSD	e3trzC4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: CSD	ECOD (1.6)
C	zf-CCHC	e3trzC3	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
C	zf-CCHC_2_like_1	e3trzC2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC_2_like_1	ECOD (1.6)
B	CSD	e3trzB4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: CSD	ECOD (1.6)
B	zf-CCHC	e3trzB3	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
B	zf-CCHC_2_like_1	e3trzB2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC_2_like_1	ECOD (1.6)
A	CSD	e3trzA4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: CSD	ECOD (1.6)
A	zf-CCHC	e3trzA3	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
A	zf-CCHC_2_like_1	e3trzA2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC_2_like_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
F	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)
E	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
E	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF21890	Lin-28A-like, second zinc knuckle (Lin-28A-like_zf-CCHC_2)	Lin-28A-like, second zinc knuckle	This domain is found at the C-terminal end of human Protein lin-28 homolog A (Lin-28A), an RNA-binding protein that inhibits processing of pre-let-7 miRNAs and regulates translation of mRNAs that control developmental timing, pluripotency and metabol ...	This domain is found at the C-terminal end of human Protein lin-28 homolog A (Lin-28A), an RNA-binding protein that inhibits processing of pre-let-7 miRNAs and regulates translation of mRNAs that control developmental timing, pluripotency and metabolism. This interaction requires the zinc-knuckle domains of Lin-28A [1-3]. This entry represents the second of these domains.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00098	Zinc knuckle (zf-CCHC)	Zinc knuckle	The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eu ...	The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00313	'Cold-shock' DNA-binding domain (CSD)	'Cold-shock' DNA-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth U], H [auth V], I [auth W], J [auth X], K [auth Y], G [auth U], H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	RNA (5'-R(GPGPGPCPAPGPGPGPAPUPUPUPUPGPCPCPCPGPGPAP*G)-3')	-	-	-
A, B, C, D, E A, B, C, D, E, F	Protein lin-28 homolog A	RNA binding binding nucleic acid binding regulatory RNA binding miRNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific mRNA binding mRNA binding protein binding translation initiation factor binding G-quadruplex RNA binding pre-miRNA binding RNA binding binding nucleic acid binding regulatory RNA binding miRNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific mRNA binding mRNA binding protein binding translation initiation factor binding G-quadruplex RNA binding pre-miRNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process pre-miRNA processing negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process RNA processing regulation of biological process negative regulation of pre-miRNA processing negative regulation of metabolic process primary metabolic process regulation of cellular process pre-miRNA processing negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process RNA processing regulation of biological process negative regulation of pre-miRNA processing negative regulation of metabolic process primary metabolic process regulation of miRNA processing regulation of gene expression miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of miRNA-mediated gene silencing post-transcriptional gene silencing miRNA processing regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of post-transcriptional gene silencing regulation of metabolic process regulation of pre-miRNA processing positive regulation of biological process RNA metabolic process regulation of miRNA-mediated gene silencing RNA biosynthetic process nucleic acid biosynthetic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of regulatory ncRNA processing regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of miRNA processing positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression cellular process protein biosynthetic process negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation regulation of translation developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development cellular response to stimulus response to stimulus homeostatic process response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis response to monosaccharide response to carbohydrate chemical homeostasis response to glucose response to chemical glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling miRNA metabolic process catabolic process miRNA catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signaling cassette positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of protein metabolic process positive regulation of translation multicellular organismal process regulation of developmental process regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development neurogenesis multicellular organism development negative regulation of neurogenesis gliogenesis regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation system development regulation of multicellular organismal development negative regulation of developmental process regulation of glial cell differentiation nervous system development negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation glial cell differentiation negative regulation of multicellular organismal process positive regulation of cytoplasmic translation cytoplasmic translation regulation of cytoplasmic translation positive regulation of neuron differentiation positive regulation of developmental process neuron differentiation positive regulation of cell differentiation generation of neurons regulation of neuron differentiation maintenance of cell number stem cell population maintenance cell population proliferation positive regulation of cell population proliferation animal organ development cell proliferation involved in kidney development regulation of cell proliferation involved in kidney development renal system development regulation of cell population proliferation kidney development positive regulation of cell proliferation involved in kidney development RNA 3'-end processing stem cell differentiation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex cytoplasmic stress granule cytosol rough endoplasmic reticulum endoplasmic reticulum endomembrane system P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR051373	Lin-28 homolog RNA-binding protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR054081	Lin-28A-like, second zinc knuckle	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002059	Cold-shock protein Csp, DNA-binding	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011129	Cold-shock domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

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.