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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC TRANSLATION INITIATION FACTOR EIF5A
 
Authors :  L. Nedyalkova, Y. Tong, W. Tempel, B. Hong, F. Mackenzie, C. H. Arrowsmi A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structur Genomics Consortium (Sgc)
Date :  31 Mar 08  (Deposition) - 15 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics Consortium, Leukemia, Apoptosis, Sgc, Hypusine, Initiation Factor, Nucleus, Protein Biosynthesis, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tong, I. Park, B. S. Hong, L. Nedyalkova, W. Tempel, H. W. Park
Crystal Structure Of Human Eif5A1: Insight Into Functional Similarity Of Human Eif5A1 And Eif5A2.
Proteins V. 75 1040 2009
PubMed-ID: 19280598  |  Reference-DOI: 10.1002/PROT.22378

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 5A-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-CODONPLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 15-151
    GeneEIF5A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEIF-5A-1, EIF-5A1, EUKARYOTIC INITIATION FACTOR 5A ISOFORM 1, EIF-5A, EIF-4D, REV-BINDING FACTOR

 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
1UNX6Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1UNX6Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1UNX-1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:99 , LEU A:101 , ARG A:109 , GLU A:110 , ASP A:111 , LEU A:112BINDING SITE FOR RESIDUE UNX A 1
2AC2SOFTWAREASP A:118 , GLU A:122BINDING SITE FOR RESIDUE UNX A 3
3AC3SOFTWARESER A:139 , GLU A:144BINDING SITE FOR RESIDUE UNX A 5

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:22 -A:73
2A:129 -B:129

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A1_HUMAN48-55  1A:48-55
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A1_HUMAN48-55  1A:48-55
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A1_HUMAN48-55  0-

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003364582ENSE00001274883chr17:7210692-7211071380IF5A1_HUMAN-00--
1.5bENST000003364585bENSE00001605087chr17:7212934-7213119186IF5A1_HUMAN1-55552A:15-55 (gaps)
B:15-44
41
30
1.6ENST000003364586ENSE00001791569chr17:7214337-7214441105IF5A1_HUMAN56-90352A:56-90
B:56-90
35
35
1.7ENST000003364587ENSE00001755330chr17:7214669-7214800132IF5A1_HUMAN91-134442A:91-134
B:91-134
44
44
1.8ENST000003364588ENSE00001615830chr17:7214897-721497074IF5A1_HUMAN135-154202A:135-150
B:135-151
16
17
1.9bENST000003364589bENSE00001525671chr17:7215141-7215782642IF5A1_HUMAN-00--

(-) 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:132
 aligned with IF5A1_HUMAN | P63241 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:136
                                    24        34        44        54        64        74        84        94       104       114       124       134       144      
          IF5A1_HUMAN    15 SATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
               SCOP domains d3cpfa1 A:15-83 automated matches                                    d3cpfa2 A:84-150 automated matches                                  SCOP domains
               CATH domains 3cpfA01 A:15-83  [code=2.30.30.30,     no name defined]              3cpfA02 A:84-150 Nucleic acid-binding proteins                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeeeeeeeee..----..eeeeeeee.....eeeeeee...eeeee..eeeeeeeeeee..eeeee.....ee......hhhhhhhhhhhhhhh...eeeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP----------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.5b  PDB: A:15-55 (gaps)           Exon 1.6  PDB: A:56-90             Exon 1.7  PDB: A:91-134 UniProt: 91-134     Exon 1.8         Transcript 1
                 3cpf A  15 SATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKT----HAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
                                    24        34        44   |    54        64        74        84        94       104       114       124       134       144      
                                                            48   53                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with IF5A1_HUMAN | P63241 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:137
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       
          IF5A1_HUMAN    15 SATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKA 151
               SCOP domains d3cpfb1 B:15-83 automated matc           hes                         d3cpfb2 B:84-151 automated matches                                   SCOP domains
               CATH domains 3cpfB01 B:15-83  [code=2.30.30           .30, no name defined]       3cpfB02 B:84-151 Nucleic acid-binding proteins                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeee....-----------..eeeee.....eeee......eeeee..eeeeeeeeeee..eeeee.............hhhhhhhhhhhhhh....eeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.5b  PDB: B:15-44 UniProt: 1-55    Exon 1.6  PDB: B:56-90             Exon 1.7  PDB: B:91-134 UniProt: 91-134     Exon 1.8          Transcript 1
                 3cpf B  15 SATFPMQCSALRKNGFVVLKGRPCKIVEMS-----------VHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKA 151
                                    24        34        44         - |      64        74        84        94       104       114       124       134       144       
                                                        44          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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IF5A1_HUMAN | P63241)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0017070    U6 snRNA binding    Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA).
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006913    nucleocytoplasmic transport    The directed movement of molecules between the nucleus and the cytoplasm.
    GO:0008612    peptidyl-lysine modification to peptidyl-hypusine    The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0006611    protein export from nucleus    The directed movement of a protein from the nucleus into the cytoplasm.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005642    annulate lamellae    Stacks of endoplasmic reticulum (ER) membranes containing a high density of nuclear pores, thought to form from excess nuclear membrane components, that have been described in a number of different cells. Annulate lamellar membranes are continuous with and embedded within the ER.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    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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 Related Entries

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UniProtKB/Swiss-Prot
        IF5A1_HUMAN | P632411fh4 5dlq

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