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(-) Description

Title :  MATURE HUMAN FRATAXIN
 
Authors :  S. Dhe-Paganon, R. Shigeta, Y. I. Chi, M. Ristow, S. E. Shoelson
Date :  08 Mar 00  (Deposition) - 08 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Freidreich'S Ataxia, Iron Transport, Mitochondrial, Disease, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Dhe-Paganon, R. Shigeta, Y. I. Chi, M. Ristow, S. E. Shoelson
Crystal Structure Of Human Frataxin.
J. Biol. Chem. V. 275 30753 2000
PubMed-ID: 10900192  |  Reference-DOI: 10.1074/JBC.C000407200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRATAXIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    FragmentRESIDUES 88-210
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1EKG)

(-) Sites  (0, 0)

(no "Site" information available for 1EKG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EKG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EKG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016065L106SFRDA_HUMANDisease (FRDA)104894105AL106S
2UniProtVAR_002428D122YFRDA_HUMANDisease (FRDA)142157346AD122Y
3UniProtVAR_002429G130VFRDA_HUMANDisease (FRDA)104894107AG130V
4UniProtVAR_002430I154FFRDA_HUMANDisease (FRDA)104894106AI154F
5UniProtVAR_002431W155RFRDA_HUMANDisease (FRDA)138471431AW155R
6UniProtVAR_008139R165CFRDA_HUMANDisease (FRDA)138034837AR165C
7UniProtVAR_008140L182FFRDA_HUMANDisease (FRDA)139616452AL182F
8UniProtVAR_016066L198RFRDA_HUMANDisease (FRDA)144104124AL198R
9UniProtVAR_049100S202CFRDA_HUMANPolymorphism1052195AS202C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FRATAXIN_2PS50810 Frataxin family profile.FRDA_HUMAN90-198  1A:90-198
2FRATAXIN_1PS01344 Frataxin family signature.FRDA_HUMAN144-158  1A:144-158

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003772701aENSE00001944433chr9:71650175-71650863689FRDA_HUMAN1-55550--
1.3aENST000003772703aENSE00001089855chr9:71661301-7166139898FRDA_HUMAN56-88330--
1.4ENST000003772704ENSE00001089856chr9:71668056-71668176121FRDA_HUMAN88-128411A:90-12839
1.5aENST000003772705aENSE00001089858chr9:71679854-7167995198FRDA_HUMAN129-161331A:129-16133
1.6dENST000003772706dENSE00001865767chr9:71687528-716891291602FRDA_HUMAN161-210501A:161-20848

(-) Sequences/Alignments

Asymmetric/Biological 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:119
 aligned with FRDA_HUMAN | Q16595 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:119
                                    99       109       119       129       139       149       159       169       179       189       199         
           FRDA_HUMAN    90 LDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGK 208
               SCOP domains d1ekga_ A: C-terminal domain of frataxin                                                                                SCOP domains
               CATH domains 1ekgA00 A:90-208 Metal Transport, Frataxin; Chain A                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.........eeeee..eeeee......eeeeeee....eeeeee...eeeeeee....eee.....hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------S---------------Y-------V-----------------------FR---------C----------------F---------------R---C------ SAPs(SNPs)
                PROSITE (1) FRATAXIN_2  PDB: A:90-198 UniProt: 90-198                                                                    ---------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------FRATAXIN_1     -------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4  PDB: A:90-128 UniProt: 88-128Exon 1.5a  PDB: A:129-161        ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.6d  PDB: A:161-208 UniProt: 161-210       Transcript 1 (2)
                 1ekg A  90 LDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGK 208
                                    99       109       119       129       139       149       159       169       179       189       199         

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EKG)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FRDA_HUMAN | Q16595)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0004322    ferroxidase activity    Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
    GO:0034986    iron chaperone activity    Assists in the delivery of iron ions to target proteins or compartments.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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).
biological process
    GO:0007628    adult walking behavior    The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
    GO:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0009792    embryo development ending in birth or egg hatching    The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
    GO:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0018283    iron incorporation into metallo-sulfur cluster    The incorporation of iron into a metallo-sulfur cluster.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0016226    iron-sulfur cluster assembly    The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0040015    negative regulation of multicellular organism growth    Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size.
    GO:0046621    negative regulation of organ growth    Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism.
    GO:0090201    negative regulation of release of cytochrome c from mitochondria    Any process that decreases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006119    oxidative phosphorylation    The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
    GO:1904234    positive regulation of aconitate hydratase activity    Any process that activates or increases the frequency, rate or extent of aconitate hydratase activity.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051349    positive regulation of lyase activity    Any process that activates or increases the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
    GO:1904231    positive regulation of succinate dehydrogenase activity    Any process that activates or increases the frequency, rate or extent of succinate dehydrogenase activity.
    GO:0019230    proprioception    The series of events by which an organism senses the position, location, orientation, and movement of the body and its parts. Proprioception is mediated by proprioceptors, sensory nerve terminals found in muscles, tendons, and joint capsules, which give information concerning movements and position of the body. The receptors in the labyrinth are sometimes also considered proprioceptors.
    GO:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
    GO:0010722    regulation of ferrochelatase activity    Any process that modulates the frequency, rate or extent of ferrochelatase activity; catalysis of the reaction: protoporphyrin + Fe2+ = protoheme + 2 H+.
    GO:0010039    response to iron 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 an iron ion stimulus.
    GO:0044281    small molecule metabolic process    The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
    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: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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FRDA_HUMAN | Q165951ly7 3s4m 3s5d 3s5e 3s5f 3t3j 3t3k 3t3l 3t3t 3t3x 5kz5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EKG)