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(-) Description

Title :  SOLUTION STRUCTURE OF THE RRM DOMAIN OF HUMAN EUKARYOTIC INITIATION FACTOR 3B
 
Authors :  L. Elantak, A. G. Tzakos, N. Locker, P. J. Lukavsky
Date :  20 Oct 06  (Deposition) - 06 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (16x)
Keywords :  Translation Initiation, Eukaryotic Initiation Factor 3 Complex, Rna Recognition Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Elantak, A. G. Tzakos, N. Locker, P. J. Lukavsky
Structure Of Eif3B Rna Recognition Motif And Its Interaction With Eif3J: Structural Insights Into The Recruitment Of Eif3B To The 40 S Ribosomal Subunit.
J. Biol. Chem. V. 282 8165 2007
PubMed-ID: 17190833  |  Reference-DOI: 10.1074/JBC.M610860200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 9
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RNA RECOGNITION MOTIF
    Gene: EIF3S9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EIF-3 ETA, EIF3 P116, EIF3 P110, EIF3B, PRT1 HOMOLOG, HPRT1

 Structural Features

(-) Chains, Units

  
NMR Structure (16x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2NLW)

(-) Sites  (0, 0)

(no "Site" information available for 2NLW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NLW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NLW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NLW)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.EIF3B_HUMAN185-268  1A:16-99

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000003970112cENSE00001920573chr7:2394517-2395055539EIF3B_HUMAN1-1671670--
1.3ENST000003970113ENSE00001597937chr7:2400345-2400537193EIF3B_HUMAN167-231651A:1-6262
1.4ENST000003970114ENSE00001668687chr7:2402280-2402399120EIF3B_HUMAN231-271411A:62-10241
1.5bENST000003970115bENSE00001798418chr7:2402705-240276258EIF3B_HUMAN271-290201A:102-1054
1.6ENST000003970116ENSE00000667963chr7:2403267-2403395129EIF3B_HUMAN291-333430--
1.7dENST000003970117dENSE00001182300chr7:2404007-2404164158EIF3B_HUMAN334-386530--
1.8bENST000003970118bENSE00000831521chr7:2405952-2406083132EIF3B_HUMAN386-430450--
1.8fENST000003970118fENSE00000831523chr7:2406160-240622667EIF3B_HUMAN430-452230--
1.8iENST000003970118iENSE00000831525chr7:2406634-240668047EIF3B_HUMAN453-468160--
1.9bENST000003970119bENSE00000831527chr7:2409107-2409317211EIF3B_HUMAN468-538710--
1.10aENST0000039701110aENSE00000831529chr7:2411412-241148473EIF3B_HUMAN539-563250--
1.11ENST0000039701111ENSE00000831531chr7:2412308-2412430123EIF3B_HUMAN563-604420--
1.12bENST0000039701112bENSE00000831533chr7:2414163-241424179EIF3B_HUMAN604-630270--
1.12dENST0000039701112dENSE00000831535chr7:2415024-2415162139EIF3B_HUMAN630-676470--
1.12fENST0000039701112fENSE00000831536chr7:2416585-2416710126EIF3B_HUMAN677-718420--
1.13cENST0000039701113cENSE00000831538chr7:2418324-241840178EIF3B_HUMAN719-744260--
1.13eENST0000039701113eENSE00000831540chr7:2418769-2418877109EIF3B_HUMAN745-781370--
1.14bENST0000039701114bENSE00001272873chr7:2419029-2419146118EIF3B_HUMAN781-814340--
1.14jENST0000039701114jENSE00001921552chr7:2419914-2420380467EIF3B_HUMAN-00--

(-) Sequences/Alignments

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
(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:105
 aligned with EIF3B_HUMAN | P55884 from UniProtKB/Swiss-Prot  Length:814

    Alignment length:105
                                   179       189       199       209       219       229       239       249       259       269     
          EIF3B_HUMAN   170 GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMT 274
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------RRM_1-2nlwA01 A:34-91                                     -------------- Pfam domains
         Sec.struct. author ................eeeee..........hhhhhhhhhhhhhhh.eeeee..........eeeeee...hhhhhhhhhh..ee.....eeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------RRM  PDB: A:16-99 UniProt: 185-268                                                  ------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-62 UniProt: 167-231 [INCOMPLETE]           ---------------------------------------1.5b Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.4  PDB: A:62-102 UniProt: 231-271 --- Transcript 1 (2)
                 2nlw A   1 GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMT 105
                                    10        20        30        40        50        60        70        80        90       100
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2NLW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NLW)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (EIF3B_HUMAN | P55884)
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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
    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:0075522    IRES-dependent viral translational initiation    Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
    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.
    GO:0075525    viral translational termination-reinitiation    A process which occurs as part of viral mRNA translation which allows expression of a downstream open reading frame (ORF) in a dicistronic mRNA. In this process, ribosomes translate the upstream ORF but following termination, a proportion of 40S subunits remain tethered to the mRNA and go on to re-initiate translation at the start codon of the downstream ORF.
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: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:0071541    eukaryotic translation initiation factor 3 complex, eIF3m    An eukaryotic translation initiation factor 3 complex that contains the PCI-domain protein eIF3m.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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        EIF3B_HUMAN | P55884: 2krb 5k1h

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