3LLH - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE FIRST DSRBD OF TAR RNA-BINDING PROTEIN 2

Authors :   S. Yamashita, M. Kawazoe, C. Takemoto, S. Sekine, M. Wakiyama, S. Yokoy

Date :   29 Jan 10 (Deposition) - 08 Dec 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Dsrbd, Dsrm, Microrna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Yamashita, T. Nagata, M. Kawazoe, C. Takemoto, Y. Muto, S. Sekine, M. Wakiyama, S. Yokoyama
The Structures Of Dsrbds Of Human Trbp
To Be Published
PubMed: search

Molecule 1 - RISC-LOADING COMPLEX SUBUNIT TARBP2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 22-105
	Gene	:	6895
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TAR RNA-BINDING PROTEIN 2, TRANS-ACTIVATION-RESPONSIVE RNA- BINDING PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MLI	1	Ligand/Ion	MALONATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MLI	-1	Ligand/Ion	MALONATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MLI	1	Ligand/Ion	MALONATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:17 , TYR A:33 , ARG A:50 , SER A:57 , CYS A:58 , THR A:59 , LYS A:69 , ARG B:26 , HOH B:110	BINDING SITE FOR RESIDUE MLI B 101

(no "SS Bond" information available for 3LLH)

(no "Cis Peptide Bond" information available for 3LLH)

(no "SAP(SNP)/Variant" information available for 3LLH)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	TRBP2_HUMAN	30-97 159-227 298-361	2	A:15-81 B:15-81 - -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	TRBP2_HUMAN	30-97 159-227 298-361	1	A:15-81 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	TRBP2_HUMAN	30-97 159-227 298-361	1	- B:15-81 - -

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000266987	1b	ENSE00000938709	chr12:53894705-53895245	541	TRBP2_HUMAN	1-18	18	0	-	-
1.3a	ENST00000266987	3a	ENSE00001767359	chr12:53895799-53895968	170	TRBP2_HUMAN	18-75	58	2	A:13-60 (gaps) B:13-60 (gaps)	48 48
1.4	ENST00000266987	4	ENSE00001148574	chr12:53896811-53896913	103	TRBP2_HUMAN	75-109	35	2	A:60-81 B:60-81	22 22
1.5	ENST00000266987	5	ENSE00001148567	chr12:53897497-53897592	96	TRBP2_HUMAN	109-141	33	0	-	-
1.6	ENST00000266987	6	ENSE00001148561	chr12:53898181-53898253	73	TRBP2_HUMAN	141-165	25	0	-	-
1.7	ENST00000266987	7	ENSE00001148552	chr12:53898482-53898599	118	TRBP2_HUMAN	166-205	40	0	-	-
1.8	ENST00000266987	8	ENSE00001148544	chr12:53898919-53899046	128	TRBP2_HUMAN	205-247	43	0	-	-
1.9	ENST00000266987	9	ENSE00001148535	chr12:53899433-53899634	202	TRBP2_HUMAN	248-315	68	0	-	-
1.10b	ENST00000266987	10b	ENSE00000938717	chr12:53899775-53900213	439	TRBP2_HUMAN	315-366	52	0	-	-

Asymmetric Unit

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)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:64
 aligned with TRBP2_HUMAN | Q15633 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:69
                                    37        47        57        67        77        87         
           TRBP2_HUMAN   28 GKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLK 96
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....eeeeeee.-----..eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DS_RBD  PDB: A:15-81 UniProt: 30-97                                 PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:13-60 (gaps) UniProt: 18-75   --------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.4  PDB: A:60-81 Transcript 1 (2)
                  3llh A 13 GKTPISLLQEYGTRIGKTPVYDLLKAE-----PNFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLK 81
                                    22        32      |  -  |     52        62        72         
                                                     39    45

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with TRBP2_HUMAN | Q15633 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:69
                                    37        47        57        67        77        87         
           TRBP2_HUMAN   28 GKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLK 96
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---dsrm-3llhB01 B:16-80                                             - Pfam domains (1)
           Pfam domains (2) ---dsrm-3llhB02 B:16-80                                             - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh....eeeeeeee.---..eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DS_RBD  PDB: B:15-81 UniProt: 30-97                                 PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: B:13-60 (gaps) UniProt: 18-75   --------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.4  PDB: B:60-81 Transcript 1 (2)
                  3llh B 13 GKTPISLLQEYGTRIGKTPVYDLLKAEG---QPNFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLK 81
                                    22        32       | - |      52        62        72         
                                                      40  44

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 3LLH)

(no "CATH Domain" information available for 3LLH)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: dsrm (27)

Homo sapiens (Human) (7)

1a	dsrm-3llhB01	B:16-80
1b	dsrm-3llhB02	B:16-80

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRBP2_HUMAN | Q15633)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0036002	pre-mRNA binding	Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule.
	GO:0070883	pre-miRNA binding	Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
	GO:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0035197	siRNA binding	Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme.
biological process
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0035280	miRNA loading onto RISC involved in gene silencing by miRNA	The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC).
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:0050689	negative regulation of defense response to virus by host	Any host process that results in the inhibition of antiviral immune response mechanisms, thereby facilitating viral replication. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	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:0045070	positive regulation of viral genome replication	Any process that activates or increases the frequency, rate or extent of viral genome replication.
	GO:0031054	pre-miRNA processing	Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
	GO:0035196	production of miRNAs involved in gene silencing by miRNA	Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
	GO:0030422	production of siRNA involved in RNA interference	Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
	GO:0006417	regulation of translation	Any process that modulates 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:0046782	regulation of viral transcription	Any process that modulates the frequency, rate or extent of the transcription of the viral genome.
	GO:0035087	siRNA loading onto RISC involved in RNA interference	The transfer of small interfering RNA molecules (siRNAs) from the Dicer family of enzymes that cleave the double-stranded RNA, onto the nuclease-containing RNA-initiated silencing complex (RISC), in the context of RNA interference.
	GO:0007338	single fertilization	The union of male and female gametes to form a zygote.
	GO:0007286	spermatid development	The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
	GO:0030423	targeting of mRNA for destruction involved in RNA interference	The process in which small interfering RNAs target cognate mRNA molecules for degradation.
cellular component
	GO:0016442	RISC complex	A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
	GO:0070578	RISC-loading complex	A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0035068	micro-ribonucleoprotein complex	A complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	3llh
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	TRBP2_HUMAN \| Q15633
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	TRBP2_HUMAN \| Q15633	:	2cpn 3adl 4wyq

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