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(-) Description

Title :  STRUCTURE OF THE HUMAN VOLTAGE-DEPENDENT ANION CHANNEL
 
Authors :  M. Bayrhuber, T. Meins, M. Habeck, S. Becker, K. Giller, S. Villinger, C. Vonrhein, C. Griesinger, M. Zweckstetter, K. Zeth
Date :  15 Aug 08  (Deposition) - 14 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Vdac, Porin, Membrane, Apoptosis, Transport, Mitochondrion Outer Membrane, Mitochondrial Outer Membrane, Membrane Protein, Host-Virus Interaction, Ion Transport, Transmembrane, Phosphoprotein, Acetylation, Mitochondrion, Cell Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bayrhuber, T. Meins, M. Habeck, S. Becker, K. Giller, S. Villinger, C. Vonrhein, C. Griesinger, M. Zweckstetter, K. Zeth
Structure Of The Human Voltage-Dependent Anion Channel.
Proc. Nat. Acad. Sci. Usa V. 105 15370 2008
PubMed-ID: 18832158  |  Reference-DOI: 10.1073/PNAS.0808115105

(-) Compounds

Molecule 1 - VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 2-283
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVOLTAGE-DEPENDENT ANION CHANNEL ISOFORM 1, VDAC-1, HVDAC1, OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1, PLASMALEMMAL PORIN, PORIN 31HL, PORIN 31HM, HUMAN VDAC

 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 2JK4)

(-) Sites  (0, 0)

(no "Site" information available for 2JK4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JK4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:81 -Asn A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JK4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EUKARYOTIC_PORINPS00558 Eukaryotic mitochondrial porin signature.VDAC1_HUMAN225-247  1A:228-250

(-) Exons   (0, 0)

(no "Exon" information available for 2JK4)

(-) 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:288
 aligned with VDAC1_HUMAN | P21796 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:288
                               1                                                                                                                                                                                                                                                                                       283  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277     |  
          VDAC1_HUMAN     - ---MAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh......eeeeeeee......eeeeeeeee....eeeeeeeeeeee....eeeeeee.....eeeeeee.......eeeeeeeee.......eeeeeeeeee..eeeeeeeeee....eeeeeeeeee..eeeeeeeeee.......eeeeeeeeee..eeeeeeee...eeeeeeee.....eeeeeeeeeee.....eeeeeeee.....eeeeeeee...eeeeeeeeee...eeeeeeeee.........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EUKARYOTIC_PORIN       -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jk4 A   1 MRGSAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQARS 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        

   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 2JK4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JK4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JK4)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VDAC1_HUMAN | P21796)
molecular function
    GO:0005253    anion channel activity    Enables the energy-independent passage of anions across a lipid bilayer down a concentration gradient.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008308    voltage-gated anion channel activity    Enables the transmembrane transfer of an anion by a voltage-gated channel. An anion is a negatively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0098656    anion transmembrane transport    A process in which an anion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006820    anion transport    The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0001662    behavioral fear response    An acute behavioral change resulting from a perceived external threat.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    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:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0006851    mitochondrial calcium ion transmembrane transport    The directed movement of calcium ions (Ca2+) into, out of or within a mitochondrion.
    GO:2000378    negative regulation of reactive oxygen species metabolic process    Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0007270    neuron-neuron synaptic transmission    The process of synaptic transmission from a neuron to another neuron across a synapse.
    GO:1903959    regulation of anion transmembrane transport    Any process that modulates the frequency, rate or extent of anion transmembrane transport.
    GO:0044070    regulation of anion transport    Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VDAC1_HUMAN | P217962k4t 5jdp 5xdn 5xdo

(-) Related Entries Specified in the PDB File

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