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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF RRM DOMAIN IN A18 HNRNP

Authors :   A. Sato, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   16 May 05 (Deposition) - 16 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Structure Genomics, Rrm Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Sato, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Rrm Domain In A18 Hnrnp
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - COLD-INDUCIBLE RNA-BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040510-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	RRM DOMAIN
	Gene	:	CIRBP, A18HNRNP, CIRP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	GLYCINE-RICH RNA-BINDING PROTEIN CIRP, A18 HNRNP


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1X5S)

(no "Site" information available for 1X5S)

(no "SS Bond" information available for 1X5S)

(no "Cis Peptide Bond" information available for 1X5S)

(no "SAP(SNP)/Variant" information available for 1X5S)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	CIRBP_HUMAN	6-84	1	A:13-91

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000320936	1a	ENSE00001643787	chr19:1269267-1269409	143	CIRBP_HUMAN	-	0	0	-	-
1.2	ENST00000320936	2	ENSE00002173545	chr19:1270927-1271035	109	CIRBP_HUMAN	1-35	35	1	A:8-42	35
1.3a	ENST00000320936	3a	ENSE00000651429	chr19:1271139-1271245	107	CIRBP_HUMAN	35-70	36	1	A:42-77	36
1.3d	ENST00000320936	3d	ENSE00000651427	chr19:1271328-1271466	139	CIRBP_HUMAN	71-117	47	1	A:78-102 (gaps)	29
1.4	ENST00000320936	4	ENSE00001616537	chr19:1271550-1271631	82	CIRBP_HUMAN	117-144	28	0	-	-
1.5a	ENST00000320936	5a	ENSE00001594551	chr19:1271980-1272050	71	CIRBP_HUMAN	144-168	25	0	-	-
1.5d	ENST00000320936	5d	ENSE00001672440	chr19:1272426-1273171	746	CIRBP_HUMAN	168-172	5	0	-	-

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)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:102
 aligned with CIRBP_HUMAN | Q14011 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:106
                                   1                                                                                                  
                                   | 3        13        23        33        43        53        63        73        83        93      
          CIRBP_HUMAN     - -------MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSRGYRGGSAG  99
               SCOP domains -------d1x5sa1 A:8-97 Cold-inducible RNA-binding protein                                         --------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------RRM_1-1x5sA01 A:15-85                                                  --------------------- Pfam domains
         Sec.struct. author .............eeeee.......hhhhhhhhhhh....eeee...........eeeee...hhhhhhhhhhh..........eeeeee.......----..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------RRM  PDB: A:13-91 UniProt: 6-84                                                --------------- PROSITE
           Transcript 1 (1) -------Exon 1.2  PDB: A:8-42 UniProt: 1-35-----------------------------------Exon 1.3d UniProt: 71-117     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3a  PDB: A:42-77             ----------------------------- Transcript 1 (2)
                 1x5s A   1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS----GPSSG 102
                                    10        20        30        40        50        60        70        80        90      |  - |    
                                                                                                                           97   98

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: Cold-inducible RNA-binding protein (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1x5sa1

A:8-97

(no "CATH Domain" information available for 1X5S)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Homo sapiens (Human) (94)

RRM_1-1x5sA01

A:15-85

NMR Structure(hide GO term definitions)

Chain A (CIRBP_HUMAN | Q14011)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003730	mRNA 3'-UTR binding	Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
	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:0070181	small ribosomal subunit rRNA binding	Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA.
	GO:0030371	translation repressor activity	Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
biological process
	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:0017148	negative regulation of translation	Any process that stops, prevents, or reduces 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: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:0009411	response to UV	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0009409	response to cold	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
	GO:0034063	stress granule assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
cellular component
	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: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: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.

NMR Structure
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Description

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