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(-) Description

Title :  CRYSTAL STRUCTURE OF EUKARYOTIC TRANSLATION INITIATION FACTOR EIF-5A2 FROM ARABIDOPSIS THALIANA
 
Authors :  Y. B. Teng, Y. X. He, Y. L. Jiang, Y. X. Chen, C. Z. Zhou
Date :  25 May 09  (Deposition) - 29 Sep 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Barrel, Alternative Splicing, Hypusine, Initiation Factor, Protein Biosynthesis, Translation, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. -B. Teng, X. -X. Ma, Y. -X. He, Y. -L. Jiang, J. Du, C. Xiang, Y. Chen, C. -Z. Zhou
Crystal Structure Of Arabidopsis Translation Initiation Factor Eif-5A2
Proteins V. 77 736 2009
PubMed-ID: 19676114  |  Reference-DOI: 10.1002/PROT.22530
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 5A-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21 DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAT1G26630.1
    Organism CommonMOUSE-EAR CRESS, THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymEIF-5A-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:21 , ASN A:25 , ILE A:26 , ARG A:27 , GLY A:30 , HOH A:188 , HOH A:247BINDING SITE FOR RESIDUE EDO A 160
2AC2SOFTWARETYR A:19 , HIS A:31 , PRO A:83 , VAL A:85 , HOH A:232BINDING SITE FOR RESIDUE EDO A 161
3AC3SOFTWARETHR A:49 , ASP A:112 , HOH A:234 , SER B:45 , HIS B:58 , HOH B:206 , HOH B:238BINDING SITE FOR RESIDUE EDO A 162
4AC4SOFTWARELYS A:115 , GLN A:148 , ILE A:149 , HOH A:209BINDING SITE FOR RESIDUE EDO A 163
5AC5SOFTWARELYS B:115 , PRO B:117 , GLN B:148 , ILE B:149 , HOH B:208 , HOH B:212BINDING SITE FOR RESIDUE EDO B 160
6AC6SOFTWARELYS A:48 , LEU B:92 , LYS B:134 , ILE B:136BINDING SITE FOR RESIDUE EDO B 161

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val B:155 -Gly B:156
2Gly B:156 -Gly B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A2_ARATH49-56
 
  2A:49-56
B:49-56
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A2_ARATH49-56
 
  1A:49-56
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A2_ARATH49-56
 
  1-
B:49-56

(-) Exons   (0, 0)

(no "Exon" information available for 3HKS)

(-) Sequences/Alignments

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:144
 aligned with IF5A2_ARATH | Q93VP3 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:144
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155    
          IF5A2_ARATH    16 SKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTAKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQMRLGFDEGKDIVVSVMSSMGEEQICAVKEVGGGK 159
               SCOP domains d3hksa1 A:16-84 automated matches                                    d3hksa2 A:85-159 automated matches                                          SCOP domains
               CATH domains 3hksA01 A:16-84  [code=2.30.30.30, no name defined]                  3hksA02 A:85-159 Nucleic acid-binding proteins                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeeeeeeeee........eeeeeeee.....eeeeeee...eeeee..eeeeeeeeee.....eeee.....ee.......hhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hks A  16 SKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTAKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQMRLGFDEGKDIVVSVMSSMGEEQICAVKEVGGGK 159
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155    

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with IF5A2_ARATH | Q93VP3 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:142
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155  
          IF5A2_ARATH    16 SKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTAKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQMRLGFDEGKDIVVSVMSSMGEEQICAVKEVGG 157
               SCOP domains d3hksb1 B:16-84 automated matches                                    d3hksb2 B:85-157 automated matches                                        SCOP domains
               CATH domains 3hksB01 B:16-84  [code=2.30.30.30, no name defined]                  3hksB02 B:85-157 Nucleic acid-binding proteins                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeeeeeeeeee......eeeeeeeee.....eeeeeee...eeeee.eeeeeeeeeee.....eeee.....ee.......hhhhhhhhhhhhhh...eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hks B  16 SKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTAKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQMRLGFDEGKDIVVSVMSSMGEEQICAVKEVGG 157
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155  

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IF5A2_ARATH | Q93VP3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0034050    host programmed cell death induced by symbiont    Cell death in a host resulting from activation of host endogenous cellular processes after direct or indirect interaction with a symbiont (defined as the smaller of two, or more, organisms engaged in symbiosis, a close interaction encompassing mutualism through parasitism). An example of direct interaction is contact with penetrating hyphae of a fungus; an example of indirect interaction is encountering symbiont-secreted molecules.
    GO:0045901    positive regulation of translational elongation    Any process that activates or increases the frequency, rate or extent of translational elongation.
    GO:0045905    positive regulation of translational termination    Any process that activates or increases the frequency, rate or extent of translational termination.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    GO:0009617    response to bacterium    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 stimulus from a bacterium.
    GO:0046686    response to cadmium ion    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 cadmium (Cd) ion stimulus.
    GO:0009611    response to wounding    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 stimulus indicating damage to the organism.
    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:0006452    translational frameshifting    A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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