3HI9 - JenaLib

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Title :   THE X-RAY CRYSTAL STRUCTURE OF THE FIRST RNA RECOGNITION MOTIF (RRM1) OF THE AU-RICH ELEMENT (ARE) BINDING PROTEIN HUR AT 2.0 ANGSTROM RESOLUTION

Authors :   R. M. Benoit, J. Kallen

Date :   19 May 09 (Deposition) - 31 Mar 10 (Release) - 07 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Beta1-Alpha1-Beta2-Beta3-Alpha2-Beta4 Topology, Methylation, Phosphoprotein, Rna-Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Benoit, N. C. Meisner, J. Kallen, P. Graff, R. Hemmig, R. Cebe, C. Ostermeier, H. Widmer, M. Auer
The X-Ray Crystal Structure Of The First Rna Recognition Motif And Site-Directed Mutagenesis Suggest A Possible Hur Redox Sensing Mechanism.
J. Mol. Biol. V. 397 1231 2010
PubMed-ID: 20219472 | Reference-DOI: 10.1016/J.JMB.2010.02.043

Molecule 1 - ELAV-LIKE PROTEIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ELAVL1, HUR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HU-ANTIGEN R, HUR

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3HI9)

(no "Site" information available for 3HI9)

(no "SS Bond" information available for 3HI9)

(no "Cis Peptide Bond" information available for 3HI9)

(no "SAP(SNP)/Variant" information available for 3HI9)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	ELAV1_HUMAN	20-98 106-186 244-322	4	A:20-96 B:20-98 C:20-96 D:20-98 - -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	ELAV1_HUMAN	20-98 106-186 244-322	1	A:20-96 - - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	ELAV1_HUMAN	20-98 106-186 244-322	1	- B:20-98 - - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	ELAV1_HUMAN	20-98 106-186 244-322	1	- - C:20-96 - - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	ELAV1_HUMAN	20-98 106-186 244-322	1	- - - D:20-98 - -

(no "Exon" information available for 3HI9)

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:79
 aligned with ELAV1_HUMAN | Q15717 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:79
                                    27        37        47        57        67        77        87         
           ELAV1_HUMAN   18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
               SCOP domains d3hi9a_ A: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: A:20-96 UniProt: 20-98                                              PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                  3hi9 A 18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
                                    27        37        47        57        67        77        87

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with ELAV1_HUMAN | Q15717 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:81
                                    27        37        47        57        67        77        87        97 
           ELAV1_HUMAN   18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 98
               SCOP domains d3hi9b_ B: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhh...eeeeee..------...eeeeee.hhhhhhhhhhhhh..ee..ee.eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: B:20-98 UniProt: 20-98                                                PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  3hi9 B 18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR------SLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 98
                                    27        37        47     |   -  |     67        77        87        97 
                                                              53     60

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with ELAV1_HUMAN | Q15717 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:79
                                    27        37        47        57        67        77        87         
           ELAV1_HUMAN   18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
               SCOP domains d3hi9c_ C: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: C:20-96 UniProt: 20-98                                              PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                  3hi9 C 18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
                                    27        37        47        57        67        77        87

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with ELAV1_HUMAN | Q15717 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:82
                                    27        37        47        57        67        77        87        97  
           ELAV1_HUMAN   18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99
               SCOP domains d3hi9d_ D: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: D:20-98 UniProt: 20-98                                               - PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  3hi9 D 18 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99
                                    27        37        47        57        67        77        87        97

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: automated matches (67)

Protein domain: automated matches (67)

Human (Homo sapiens) [TaxId: 9606] (56)

1a	d3hi9a_	A:
1b	d3hi9b_	B:
1c	d3hi9c_	C:
1d	d3hi9d_	D:

(no "CATH Domain" information available for 3HI9)

(no "Pfam Domain" information available for 3HI9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ELAV1_HUMAN | Q15717)

molecular function
	GO:0017091	AU-rich element binding	Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
	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:0035925	mRNA 3'-UTR AU-rich region binding	Interacting selectively and non-covalently with a region containing frequent adenine and uridine bases within the 3' untranslated region of a mRNA molecule.
	GO:0003730	mRNA 3'-UTR binding	Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
	GO:0070935	3'-UTR-mediated mRNA stabilization	An mRNA stabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0048255	mRNA stabilization	Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	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:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
	GO:2000036	regulation of stem cell population maintenance	Any process that modulates the frequency, rate or extent of stem cell population maintenance.
cellular component
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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	3hi9
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	ELAV1_HUMAN \| Q15717	:	4ed5 4egl 4fxv

1fxl	CRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE C-FOS RNA

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