2LI8 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   THE SOLUTION STRUCTURE OF THE LIN28-ZNF DOMAINS BOUND TO AGGAGAU OF PRE-LET-7 MIRNA

Authors :   F. H. -T. Allain, F. E. Loughlin

Date :   25 Aug 11 (Deposition) - 07 Dec 11 (Release) - 25 Jan 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Zinc Finger, Micro Rna, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. E. Loughlin, L. F. Gebert, H. Towbin, A. Brunschweiger, J. Hall, F. H. Allain
Structural Basis Of Pre-Let-7 Mirna Recognition By The Zinc Knuckles Of Pluripotency Factor Lin28.
Nat. Struct. Mol. Biol. V. 19 84 2011
PubMed-ID: 22157959 | Reference-DOI: 10.1038/NSMB.2202

Molecule 1 - PROTEIN LIN-28 HOMOLOG A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)CODON PLUS
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Fragment	:	CCHC-TYPE 1 AND CCHC-TYPE 1 ZINC FINGER DOMAIN RESIDUES 124-186
	Gene	:	CSDD1, LIN-28A, LIN28, LIN28A, ZCCHC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LIN-28A, ZINC FINGER CCHC DOMAIN-CONTAINING PROTEIN 1

*Molecule 2 - RNA (5'-R(APGPGPAPGPAPU)-3')**
	Chains	:	B
	Engineered	:	YES
	Fragment	:	HSA-PRE-LET-7G TERMINAL LOOP
	Synthetic	:	YES

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

NMR Structure * (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:139 , CYS A:142 , HIS A:147 , CYS A:152	BINDING SITE FOR RESIDUE ZN A 187
2	AC2	SOFTWARE	CYS A:161 , CYS A:164 , HIS A:169 , CYS A:174	BINDING SITE FOR RESIDUE ZN A 188

(no "SS Bond" information available for 2LI8)

(no "Cis Peptide Bond" information available for 2LI8)

(no "SAP(SNP)/Variant" information available for 2LI8)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_CCHC	PS50158	Zinc finger CCHC-type profile.	LN28A_HUMAN	138-153	1	A:138-153

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_CCHC	PS50158	Zinc finger CCHC-type profile.	LN28A_HUMAN	138-153	1	A:138-153

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000326279	1a	ENSE00001462763	chr1:26737269-26737413	145	LN28A_HUMAN	1-11	11	0	-	-
1.2	ENST00000326279	2	ENSE00000902186	chr1:26737877-26738073	197	LN28A_HUMAN	11-76	66	0	-	-
1.3	ENST00000326279	3	ENSE00000902185	chr1:26751794-26751978	185	LN28A_HUMAN	77-138	62	1	A:124-138	15
1.4b	ENST00000326279	4b	ENSE00001462759	chr1:26752733-26756213	3481	LN28A_HUMAN	138-209	72	1	A:138-186	49

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:63
 aligned with LN28A_HUMAN | Q9H9Z2 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:63
                                   133       143       153       163       173       183   
          LN28A_HUMAN   124 PKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQG 186
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................hhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------ZF_CCHC         --------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3       ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.4b  PDB: A:138-186 UniProt: 138-209        Transcript 1 (2)
                 2li8 A 124 PKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQG 186
                                   133       143       153       163       173       183

Chain B from PDB  Type:RNA  Length:7
                                       
                 2li8 B   1 AGGAGAU   7

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2LI8)

(no "CATH Domain" information available for 2LI8)

(no "Pfam Domain" information available for 2LI8)

NMR Structure(hide GO term definitions)

Chain A (LN28A_HUMAN | Q9H9Z2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035198	miRNA binding	Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0031369	translation initiation factor binding	Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0031123	RNA 3'-end processing	Any process involved in forming the mature 3' end of an RNA molecule.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0007281	germ cell development	The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
	GO:0010587	miRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
	GO:0010586	miRNA metabolic process	The chemical reactions and pathways involving miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
	GO:0045686	negative regulation of glial cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation.
	GO:1901724	positive regulation of cell proliferation involved in kidney development	Any process that activates or increases the frequency, rate or extent of cell proliferation involved in kidney development.
	GO:0045666	positive regulation of neuron differentiation	Any process that activates or increases the frequency, rate or extent of neuron differentiation.
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0031054	pre-miRNA processing	Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
	GO:0060964	regulation of gene silencing by miRNA	Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0035019	somatic stem cell population maintenance	Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
	GO:0048863	stem cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
	GO:0019827	stem cell population maintenance	The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

NMR Structure
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	2li8
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	LN28A_HUMAN \| Q9H9Z2	:	2cqf 5udz

2cqf	STRUCTURE OF LIN28 ZNFS FREE FORM RELATED ID: 17883 RELATED DB: BMRB

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