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(-) Description

Title :  NMR STRUCTURE OF BNIP3 TRANSMEMBRANE DOMAIN IN LIPID BICELLES
 
Authors :  E. V. Bocharov, Y. E. Pustovalova, P. E. Volynsky, I. V. Maslennikov, M. V. Goncharuk, Y. S. Ermolyuk, A. S. Arseniev
Date :  14 Sep 06  (Deposition) - 17 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (16x)
Keywords :  Membrane Protein, Mitochondrion, Transmembrane, Transmembrane Domain, Bcl-2, Bnip3, Membrane, Homodimer, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. V. Bocharov, Y. E. Pustovalova, K. V. Pavlov, P. E. Volynsky, M. V. Goncharuk, Y. S. Ermolyuk, D. V. Karpunin, A. A. Schulga, M. P. Kirpichnikov, R. G. Efremov, I. V. Maslennikov, A. S. Arseniev
Unique Dimeric Structure Of Bnip3 Transmembrane Domain Suggests Membrane Permeabilization As A Cell Death Trigger.
J. Biol. Chem. V. 282 16256 2007
PubMed-ID: 17412696  |  Reference-DOI: 10.1074/JBC.M701745200

(-) Compounds

Molecule 1 - BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System VectorPGEMEX1
    FragmentHOMODIMERIC TRANSMEMBRANE DOMAIN, RESIDUES 146-190
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsMITOCHONDIONAL PROTEIN FROM BCL-2 FAMILY
    SynonymBNIP3 TM

 Structural Features

(-) Chains, Units

  
NMR Structure (16x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2J5D)

(-) Sites  (0, 0)

(no "Site" information available for 2J5D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J5D)

(-) Exons   (0, 0)

(no "Exon" information available for 2J5D)

(-) Sequences/Alignments

NMR Structure
   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:45
 aligned with BNIP3_HUMAN | Q12983 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:45
                                   220       230       240       250     
          BNIP3_HUMAN   211 RNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTS 255
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ............................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 2j5d A 146 RNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTS 190
                                   155       165       175       185     

Chain B from PDB  Type:PROTEIN  Length:45
 aligned with BNIP3_HUMAN | Q12983 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:45
                                   220       230       240       250     
          BNIP3_HUMAN   211 RNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTS 255
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ............................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 2j5d B 146 RNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTS 190
                                   155       165       175       185     

   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 2J5D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J5D)

(-) Gene Ontology  (56, 56)

NMR Structure(hide GO term definitions)
Chain A,B   (BNIP3_HUMAN | Q12983)
molecular function
    GO:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0048102    autophagic cell death    A form of programmed cell death that is accompanied by the formation of autophagosomes. Autophagic cell death is characterized by lack of chromatin condensation and massive vacuolization of the cytoplasm, with little or no uptake by phagocytic cells.
    GO:0000422    autophagy of mitochondrion    The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
    GO:0050873    brown fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0071279    cellular response to cobalt ion    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 cobalt ion stimulus.
    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:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0071260    cellular response to mechanical stimulus    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 mechanical stimulus.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0008626    granzyme-mediated apoptotic signaling pathway    A series of molecular signals induced by granzymes which triggers the apoptotic death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of apoptosis is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce apoptosis in target cells.
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:1990144    intrinsic apoptotic signaling pathway in response to hypoxia    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to hypoxia (lowered oxygen tension). Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. The pathway ends when the execution phase of apoptosis is triggered.
    GO:0043653    mitochondrial fragmentation involved in apoptotic process    The change in the morphology of the mitochondria in an apoptotic cell from a highly branched network to a fragmented vesicular form.
    GO:0097345    mitochondrial outer membrane permeabilization    The process by which the mitochondrial outer membrane becomes permeable to the passing of proteins and other molecules from the intermembrane space to the cytosol as part of the apoptotic signaling pathway.
    GO:0035694    mitochondrial protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a mitochondrial protein. This process is necessary to maintain the healthy state of mitochondria and is thought to occur via the induction of an intramitochondrial lysosome-like organelle that acts to eliminate the damaged oxidised mitochondrial proteins without destroying the mitochondrial structure.
    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:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0045837    negative regulation of membrane potential    Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0010637    negative regulation of mitochondrial fusion    Any process that decreases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment.
    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:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010508    positive regulation of autophagy    Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0010666    positive regulation of cardiac muscle cell apoptotic process    Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
    GO:0016239    positive regulation of macroautophagy    Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
    GO:0090141    positive regulation of mitochondrial fission    Any process that increases the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:0043068    positive regulation of programmed cell death    Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    GO:0043243    positive regulation of protein complex disassembly    Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases 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:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:1903715    regulation of aerobic respiration    Any process that modulates the frequency, rate or extent of aerobic respiration.
    GO:0046902    regulation of mitochondrial membrane permeability    Any process that modulates the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane.
    GO:0010821    regulation of mitochondrion organization    Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.
    GO:0055093    response to hyperoxia    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 increased oxygen tension.
    GO:0001666    response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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: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:0031307    integral component of mitochondrial outer membrane    The component of the mitochondrial outer membrane consisting of the gene products 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:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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

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

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        BNIP3_HUMAN | Q129832ka1 2ka2

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