3NS6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HTE RNA RECOGNITION MOTIF OF YEAST EIF3B RESIDUES 76-170

Authors :   S. Khoshnevis, P. Neumann, R. Ficner

Date :   01 Jul 10 (Deposition) - 06 Oct 10 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

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

Keywords :   Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Khoshnevis, P. Neumann, R. Ficner
Crystal Structure Of The Rna Recognition Motif Of Yeast Translation Initiation Factor Eif3B Reveals Differences To Human Eif3B.
Plos One V. 5 12784 2010
PubMed-ID: 20862284 | Reference-DOI: 10.1371/JOURNAL.PONE.0012784

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 76-170
	Gene	:	CDC63, PRT1, YOR361C
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	EIF3B, EUKARYOTIC TRANSLATION INITIATION FACTOR 3 90 KDA SUBUNIT, EIF3 P90, TRANSLATION INITIATION FACTOR EIF3 P90 SUBUNIT, CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:67 , LYS A:105 , ARG A:154 , HOH A:189 , HOH A:244 , HOH A:356 , HOH A:357 , ARG B:154	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	LYS A:152 , HOH A:247 , LYS B:91 , SER B:133 , ASN B:135	BINDING SITE FOR RESIDUE SO4 A 4
3	AC3	SOFTWARE	LYS B:147 , ARG B:148 , ARG B:154 , HOH B:395	BINDING SITE FOR RESIDUE SO4 B 2
4	AC4	SOFTWARE	LYS A:161 , ARG A:165 , HOH A:188 , HOH A:282 , PRO B:93 , LYS B:96 , HOH B:186	BINDING SITE FOR RESIDUE SO4 B 3

(no "SS Bond" information available for 3NS6)

(no "Cis Peptide Bond" information available for 3NS6)

(no "SAP(SNP)/Variant" information available for 3NS6)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	EIF3B_YEAST	77-162	2	A:77-162 B:77-162

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.	EIF3B_YEAST	77-162	1	A:77-162 -

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.	EIF3B_YEAST	77-162	1	- B:77-162

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	EIF3B_YEAST	77-162	2	A:77-162 B:77-162

(no "Exon" information available for 3NS6)

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:99
 aligned with EIF3B_YEAST | P06103 from UniProtKB/Swiss-Prot  Length:763

    Alignment length:99
                                    80        90       100       110       120       130       140       150       160         
          EIF3B_YEAST    71 EEFNFDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSD 169
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeee.....hhhhhhhhhhhhhhhhhh...eeeee..ee....ee..eeeeee.hhhhhhhhhhhhh..........eeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RRM  PDB: A:77-162 UniProt: 77-162                                                    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3ns6 A  71 GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSD 169
                                    80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with EIF3B_YEAST | P06103 from UniProtKB/Swiss-Prot  Length:763

    Alignment length:99
                                    80        90       100       110       120       130       140       150       160         
          EIF3B_YEAST    71 EEFNFDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSD 169
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------RRM_1-3ns6B01 B:94-153                                      ---------------- Pfam domains (1)
           Pfam domains (2) -----------------------RRM_1-3ns6B02 B:94-153                                      ---------------- Pfam domains (2)
         Sec.struct. author ...hhh.eeeee.....hhhhhhhhhhhhhhhhhh...eeeee..ee....ee..eeeeee.hhhhhhhhhhhhh..eee..ee.eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RRM  PDB: B:77-162 UniProt: 77-162                                                    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3ns6 B  71 GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSD 169
                                    80        90       100       110       120       130       140       150       160

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 3NS6)

(no "CATH Domain" information available for 3NS6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (16)

1a	RRM_1-3ns6B01	B:94-153
1b	RRM_1-3ns6B02	B:94-153

Asymmetric Unit(hide GO term definitions)

Chain A,B (EIF3B_YEAST | P06103)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
	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.
biological process
	GO:0002183	cytoplasmic translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
	GO:0001731	formation of translation preinitiation complex	The joining of the small ribosomal subunit, ternary complex, and mRNA.
	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: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:0016282	eukaryotic 43S preinitiation complex	A protein complex composed of the 40S ribosomal subunit plus eIF1A, eIF3, and eIF2-GTP-bound methionyl-initiator methionine tRNA.
	GO:0033290	eukaryotic 48S preinitiation complex	A protein complex composed of the small ribosomal subunit, eIF3, eIF1A, methionyl-initiatior methionine and a capped mRNA. The complex is initially positioned at the 5'-end of the capped mRNA.
	GO:0005852	eukaryotic translation initiation factor 3 complex	A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs.
	GO:0043614	multi-eIF complex	A multifactor complex composed of multiple translation initiation factors and the initiatior tRNAiMet, which is ready to bind to the small (40S) ribosome to form the 43S preinitiation complex. In S. cerevisiae, this complex is composed of eIF1, eIF2, eIF3, and eIF5.

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	EIF3B_YEAST \| P06103	:	3jap 3jaq 3ns5 3zwl 4u1e 4u1f

3ns5	CRYSTAL STRUCTURE OF THE RNA RECOGNITION MOTIF OF YEAST EIF3B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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