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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE RNA BINDING DOMAIN OF EUKARYOTIC INITIATION FACTOR 4B

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

Date :   28 May 04 (Deposition) - 28 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Rna Recognition Motif, Rrm, Rna Binding Domain, Rbd, Rnp, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Suzuki, Y. Muto, T. Nagata, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Rna Binding Domain Of Eukaryotic Initiation Factor 4B
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4B
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040301-18
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA RECOGNITION MOTIF
	Gene	:	RIKEN CDNA ADSE02039
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	EIF-4B


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1WI8)

(no "Site" information available for 1WI8)

(no "SS Bond" information available for 1WI8)

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Pro A:94	-	Pro A:95

(no "SAP(SNP)/Variant" information available for 1WI8)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	IF4B_HUMAN	96-173	1	A:96-173

NMR Structure (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000262056	1	ENSE00001532938	chr12:53400062-53400280	219	IF4B_HUMAN	1-5	5	0	-	-
1.2	ENST00000262056	2	ENSE00000919949	chr12:53410257-53410394	138	IF4B_HUMAN	5-51	47	1	A:81-86	6
1.3b	ENST00000262056	3b	ENSE00000838122	chr12:53412582-53412790	209	IF4B_HUMAN	51-120	70	1	A:87-120	34
1.4	ENST00000262056	4	ENSE00000838123	chr12:53413694-53413810	117	IF4B_HUMAN	121-159	39	1	A:121-159	39
1.5	ENST00000262056	5	ENSE00000746225	chr12:53415590-53415644	55	IF4B_HUMAN	160-178	19	1	A:160-178	19
1.6	ENST00000262056	6	ENSE00000746227	chr12:53416277-53416411	135	IF4B_HUMAN	178-223	46	1	A:178-178	1
1.7b	ENST00000262056	7b	ENSE00000838124	chr12:53421566-53421703	138	IF4B_HUMAN	223-269	47	1	A:179-181	3
1.8a	ENST00000262056	8a	ENSE00000838125	chr12:53421799-53421972	174	IF4B_HUMAN	269-327	59	1	A:182-184	3
1.9	ENST00000262056	9	ENSE00000746234	chr12:53427590-53427818	229	IF4B_HUMAN	327-403	77	0	-	-
1.10a	ENST00000262056	10a	ENSE00000746237	chr12:53428396-53428493	98	IF4B_HUMAN	403-436	34	0	-	-
1.11	ENST00000262056	11	ENSE00000746239	chr12:53431193-53431406	214	IF4B_HUMAN	436-507	72	0	-	-
1.12	ENST00000262056	12	ENSE00000746241	chr12:53432140-53432195	56	IF4B_HUMAN	507-526	20	0	-	-
1.13	ENST00000262056	13	ENSE00000838126	chr12:53433022-53433127	106	IF4B_HUMAN	526-561	36	0	-	-
1.14	ENST00000262056	14	ENSE00000746245	chr12:53433414-53433486	73	IF4B_HUMAN	561-585	25	0	-	-
1.15	ENST00000262056	15	ENSE00001309333	chr12:53433927-53435992	2066	IF4B_HUMAN	586-611	26	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:104
 aligned with IF4B_HUMAN | P23588 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:252
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275  
           IF4B_HUMAN    26 GTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSG 277
               SCOP domains d1wi8a                                                       _ A: Eukaryotic translation initiation factor 4B                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------RRM_1-1wi8A01 A:98-167                                                -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-------------------------------------------------------.........eeeeee......hhhhhhhhh....eeeee..............eeeee.hhhhhhhhhhhhh.ee..ee.eeee........----------------------------------------------------------------...-----------------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------RRM  PDB: A:96-173 UniProt: 96-173                                            -------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:81-86    ---------------------------------------------------------------------Exon 1.4  PDB: A:121-159               Exon 1.5           --------------------------------------------Exon 1.7b  PDB: A:179-181 UniProt: 223-269     -------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.3b  PDB: A:87-120 UniProt: 51-120 [INCOMPLETE]                 ---------------------------------------------------------Exon 1.6  PDB: A:178-178 UniProt: 178-223     ---------------------------------------------Exon 1.8a Transcript 1 (2)
                 1wi8 A  81 GSSGSS-------------------------------------------------------GSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKD----------------------------------------------------------------SGP-----------------------------SSG 184
                                 |   -         -         -         -         -         - |      95       105       115       125       135       145       155       165       175  |      -         -         -         -         -         -       181         -         -       182  
                                86                                                      87                                                                                        178                                                              179 |                           182  
                                                                                                                                                                                                                                                     181

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: Eukaryotic translation initiation factor 4B (1)

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

d1wi8a_

(no "CATH Domain" information available for 1WI8)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Homo sapiens (Human) (94)

RRM_1-1wi8A01

A:98-167

NMR Structure(hide GO term definitions)

Chain A (IF4B_HUMAN | P23588)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0033592	RNA strand annealing activity	Facilitates the base-pairing of complementary single-stranded RNA.
	GO:0034057	RNA strand-exchange activity	Facilitates the displacement of one strand of an RNA-RNA duplex and its replacement with a different strand of higher complementarity.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0043024	ribosomal small subunit binding	Interacting selectively and non-covalently with any part of the small ribosomal subunit.
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0002181	cytoplasmic translation	The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
	GO:0097010	eukaryotic translation initiation factor 4F complex assembly	The aggregation, arrangement and bonding together of a set of components to form the eukaryotic translation initiation factor 4F complex.
	GO:0001731	formation of translation preinitiation complex	The joining of the small ribosomal subunit, ternary complex, and mRNA.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0006446	regulation of translational initiation	Any process that modulates the frequency, rate or extent of translational initiation.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	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:0016281	eukaryotic translation initiation factor 4F complex	The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.
	GO:0005844	polysome	A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

NMR Structure
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	Cis Peptide Bonds
		Pro A:94 - Pro A:95	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 20)

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Exons (7, 7)

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