Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE FULL LENGTH EIF5A FROM SACCHAROMYCES CEREVISIAE
 
Authors :  M. Sanches, C. A. O. Dias, L. H. Aponi, S. R. Valentini, B. Guimaraes
Date :  01 Oct 08  (Deposition) - 02 Dec 08  (Release) - 02 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Translation Initiation Factor, Yeast, Low Resolution, Acetylation, Hypusine, Initiation Factor, Phosphoprotein, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sanches, C. A. O. Dias, L. H. Aponi, S. R. Valentini, B. Guimaraes
Crystal Structure Of The Full Length Eif5A From Saccharomyces Cerevisiae
To Be Published
PubMed: search
(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 PlasmidPQE30
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHYP2, TIF51A, YEL034W, SYGP-ORF21
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymEIF-5A-2, EIF-4D, HYPUSINE-CONTAINING PROTEIN HP2

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ER0)

(-) Sites  (0, 0)

(no "Site" information available for 3ER0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ER0)

(-) Cis Peptide Bonds  (19, 19)

Asymmetric Unit
No.Residues
1Gly A:14 -Ser A:15
2Ser A:16 -Ala A:17
3Ala A:17 -Thr A:18
4His A:52 -Gly A:53
5Ile A:95 -Asp A:96
6Asp A:96 -Asp A:97
7Gly A:98 -Phe A:99
8Leu A:100 -Ser A:101
9Thr A:109 -Lys A:110
10Gly A:118 -Glu A:119
11Ala B:17 -Thr B:18
12Thr B:49 -Gly B:50
13Ile B:95 -Asp B:96
14Asp B:96 -Asp B:97
15Gly B:98 -Phe B:99
16Leu B:100 -Ser B:101
17Thr B:109 -Lys B:110
18Gly B:118 -Glu B:119
19Glu B:130 -Gly B:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ER0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A1_YEAST49-56
 
  2A:49-56
B:49-56
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A1_YEAST49-56
 
  1A:49-56
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A1_YEAST49-56
 
  1-
B:49-56

(-) Exons   (0, 0)

(no "Exon" information available for 3ER0)

(-) 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:146
 aligned with IF5A1_YEAST | P23301 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:146
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151      
          IF5A1_YEAST    12 DAGSSATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHLVAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLMVTIISAMGEEAAISFKEAARTD 157
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3er0A01 A:12-84  [code=2.30.30.30, no name defined]                      3er0A02 A:85-157 Nucleic acid-binding proteins                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee........eeee..eeeeeeeeeee........eeeeeeee......eeeeee...eeee....eeeee...........................hhhhhhhhh.......eeeeeee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------IF5A_HYP----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3er0 A  12 DAGSSATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHLVAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLMVTIISAMGEEAAISFKEAARTD 157
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151      

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with IF5A1_YEAST | P23301 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:135
                                    26        36        46        56        66        76        86        96       106       116       126       136       146     
          IF5A1_YEAST    17 ATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHLVAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLMVTIISAMGEEAAISFK 151
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3er0B01 B:17-84  [code=2.30.30.30,     no name defined]             3er0B02 B:85-151 Nucleic acid-binding proteins                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eee....eeeeeeeee.....----.eeeeeee......eeeee....eeee....eeeee...........................hhhhhhhhh.......eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------IF5A_HYP----------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3er0 B  17 ATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGK----KVHLVAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLMVTIISAMGEEAAISFK 151
                                    26        36        46    |   56        66        76        86        96       106       116       126       136       146     
                                                             51   56                                                                                               

   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 3ER0)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ER0)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IF5A1_YEAST | P23301)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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:1903272    positive regulation of cytoplasmic translational elongation through polyproline stretches    Any process that activates or increases the frequency, rate or extent of cytoplasmic translational elongation through polyproline stretches.
    GO:0045901    positive regulation of translational elongation    Any process that activates or increases the frequency, rate or extent of translational elongation.
    GO:0045948    positive regulation of translational initiation    Any process that activates or increases the frequency, rate or extent of translational initiation.
    GO:0045905    positive regulation of translational termination    Any process that activates or increases the frequency, rate or extent of translational termination.
    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:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0022626    cytosolic ribosome    A ribosome located in the cytosol.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3er0)
 
  Sites
(no "Sites" information available for 3er0)
 
  Cis Peptide Bonds
    Ala A:17 - Thr A:18   [ RasMol ]  
    Ala B:17 - Thr B:18   [ RasMol ]  
    Asp A:96 - Asp A:97   [ RasMol ]  
    Asp B:96 - Asp B:97   [ RasMol ]  
    Glu B:130 - Gly B:131   [ RasMol ]  
    Gly A:118 - Glu A:119   [ RasMol ]  
    Gly A:14 - Ser A:15   [ RasMol ]  
    Gly A:98 - Phe A:99   [ RasMol ]  
    Gly B:118 - Glu B:119   [ RasMol ]  
    Gly B:98 - Phe B:99   [ RasMol ]  
    His A:52 - Gly A:53   [ RasMol ]  
    Ile A:95 - Asp A:96   [ RasMol ]  
    Ile B:95 - Asp B:96   [ RasMol ]  
    Leu A:100 - Ser A:101   [ RasMol ]  
    Leu B:100 - Ser B:101   [ RasMol ]  
    Ser A:16 - Ala A:17   [ RasMol ]  
    Thr A:109 - Lys A:110   [ RasMol ]  
    Thr B:109 - Lys B:110   [ RasMol ]  
    Thr B:49 - Gly B:50   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3er0
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IF5A1_YEAST | P23301
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  IF5A1_YEAST | P23301
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IF5A1_YEAST | P233015dat 5dc3 5dge 5dgf 5gak 5mc6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ER0)