Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF MOUSE A1 BOUND TO THE BID BH3-DOMAIN
 
Authors :  C. Smits, P. E. Czabotar, M. G. Hinds, C. L. Day
Date :  17 Feb 08  (Deposition) - 04 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, Bh3, Bcl-2, Membrane, Apoptosis, Pro-Survival, Mitochondrion, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Smits, P. E. Czabotar, M. G. Hinds, C. L. Day
Structural Plasticity Underpins Promiscuous Binding Of The Prosurvival Protein A1.
Structure V. 16 818 2008
PubMed-ID: 18462686  |  Reference-DOI: 10.1016/J.STR.2008.02.009

(-) Compounds

Molecule 1 - BCL-2-RELATED PROTEIN A1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX 6P-3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantPSJS 1240
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-152
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPROTEIN BFL-1, HEMOPOIETIC-SPECIFIC EARLY RESPONSE PROTEIN, A1-A
 
Molecule 2 - BH3-INTERACTING DOMAIN DEATH AGONIST P13
    ChainsB
    FragmentBH3-DOMAIN, RESIDUES 76-109
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymBH3-INTERACTING DOMAIN DEATH AGONIST, P13 BID
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:10 , HOH A:2001BINDING SITE FOR RESIDUE CL A1150

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCL2_FAMILYPS50062 BCL2-like apoptosis inhibitors family profile.B2LA1_MOUSE37-142  1A:37-142
2BH1PS01080 Apoptosis regulator, Bcl-2 family BH1 motif signature.B2LA1_MOUSE78-97  1A:78-97
3BH3PS01259 Apoptosis regulator, Bcl-2 family BH3 motif signature.BID_MOUSE86-100  1B:86-100
4BH2PS01258 Apoptosis regulator, Bcl-2 family BH2 motif signature.B2LA1_MOUSE133-144  1A:133-144

(-) Exons   (0, 0)

(no "Exon" information available for 2VOI)

(-) 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:150
 aligned with B2LA1_MOUSE | Q07440 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:150
                             1                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
          B2LA1_MOUSE     - -MAESELMHIHSLAEHYLQYVLQVPAFESAPSQACRVLQRVAFSVQKEVEKNLKSYLDDFHVESIDTARIIFNQVMEKEFEDGIINWGRIVTIFAFGGVLLKKLPQEQIALDVCAYKQVSSFVAEFIMNNTGEWIRQNGGWEDGFIKKFE 149
               SCOP domains d2voia_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------Bcl-2-2voiA01 A:37-140                                                                                  --------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------------BCL2_FAMILY  PDB: A:37-142 UniProt: 37-142                                                                ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------BH1  PDB: A:78-97   -----------------------------------BH2         ----- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2voi A   0 SMAESELMHIHSLAEHYLQYVLQVPAFESAPSQACRVLQRVAFSVQKEVEKNLKSYLDDFHVESIDTARIIFNQVMEKEFEDGIINWGRIVTIFAFGGVLLKKLKQEQIALDVSAYKQVSSFVAEFIMNNTGEWIRQNGGWEDGFIKKFE 149
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain B from PDB  Type:PROTEIN  Length:24
 aligned with BID_MOUSE | P70444 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:24
                                    87        97    
            BID_MOUSE    78 SQEEIIHNIARHLAQIGDEMDHNI 101
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains BID-2voiB01 B:78-101     Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------ PROSITE (2)
                PROSITE (3) --------BH3            - PROSITE (3)
                 Transcript ------------------------ Transcript
                 2voi B  78 SQEEIIHNIARHLAQIGDEMDHNI 101
                                    87        97    

   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  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (44, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B2LA1_MOUSE | Q07440)
molecular function
    GO:0015267    channel activity    Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
    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:0001782    B cell homeostasis    The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    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:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0008053    mitochondrial fusion    Merging of two or more mitochondria within a cell to form a single compartment.
    GO:0002903    negative regulation of B cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell apoptotic process.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0001836    release of cytochrome c from mitochondria    The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
    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
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.

Chain B   (BID_MOUSE | P70444)
molecular function
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0008637    apoptotic mitochondrial changes    The morphological and physiological alterations undergone by mitochondria during apoptosis.
    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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0090150    establishment of protein localization to membrane    The directed movement of a protein to a specific location in a membrane.
    GO:0097191    extrinsic apoptotic signaling pathway    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
    GO:0034349    glial cell apoptotic process    Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system.
    GO:0097284    hepatocyte apoptotic process    Any apoptotic process in a hepatocyte, the main structural component of the liver.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:2001238    positive regulation of extrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0032464    positive regulation of protein homooligomerization    Any process that activates or increases the frequency, rate or extent of protein homooligomerization.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    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:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:2000045    regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:1902108    regulation of mitochondrial membrane permeability involved in apoptotic process    Any regulation of mitochondrial membrane permeability that is involved in apoptotic process.
    GO:0032459    regulation of protein oligomerization    Any process that modulates the frequency, rate or extent of protein oligomerization.
    GO:0001836    release of cytochrome c from mitochondria    The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0042770    signal transduction in response to DNA damage    A cascade of processes induced by the detection of DNA damage within a cell.
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: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:0032592    integral component of mitochondrial membrane    The component of the mitochondrial 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:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2voi)
 

(-) 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
  2voi
    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
  B2LA1_MOUSE | Q07440
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  BID_MOUSE | P70444
    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
  B2LA1_MOUSE | Q07440
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  BID_MOUSE | P70444
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        B2LA1_MOUSE | Q074402vof 2vog 2voh
        BID_MOUSE | P704441ddb

(-) Related Entries Specified in the PDB File

2vof STRUCTURE OF MOUSE A1 BOUND TO THE PUMA BH3-DOMAIN
2vog STRUCTURE OF MOUSE A1 BOUND TO THE BMF BH3-DOMAIN
2voh STRUCTURE OF MOUSE A1 BOUND TO THE BAK BH3-DOMAIN