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(-) Description

Title :  STRUCTURE OF MOUSE A1 BOUND TO THE BMF 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 :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, Bh3, Bcl-2, Apoptosis, Pro-Survival (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
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX 6P-3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PSJS 1240
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-152
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PROTEIN BFL-1, HEMOPOIETIC-SPECIFIC EARLY RESPONSE PROTEIN, A1-A
 
Molecule 2 - BCL-2-MODIFYING FACTOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET31B BMF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BH3-DOMAIN, RESIDUES 126-152
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: C-TERMINAL HOMOSERINE LACTONE DUE TO CNBR CLEAVAGE.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:86 , GLY A:87 , HOH A:2026 , HIS B:146BINDING SITE FOR RESIDUE CL A1150
2AC2SOFTWAREMET A:7 , HIS A:10BINDING SITE FOR RESIDUE CL A1151

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 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
3BH2PS01258 Apoptosis regulator, Bcl-2 family BH2 motif signature.B2LA1_MOUSE133-144  1A:133-144

(-) Exons   (0, 0)

(no "Exon" information available for 2VOG)

(-) 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:145
 aligned with B2LA1_MOUSE | Q07440 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:151
                              1                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148 
          B2LA1_MOUSE     - --MAESELMHIHSLAEHYLQYVLQVPAFESAPSQACRVLQRVAFSVQKEVEKNLKSYLDDFHVESIDTARIIFNQVMEKEFEDGIINWGRIVTIFAFGGVLLKKLPQEQIALDVCAYKQVSSFVAEFIMNNTGEWIRQNGGWEDGFIKKFE 149
               SCOP domains d2voga_ A: automated match      es                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------Bcl-2-2vogA01 A:37-140                                                                                  --------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...------hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh 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
                 2vog A  -1 GSMAESELMHIHSLAEHYLQYVLQVP------SQACRVLQRVAFSVQKEVEKNLKSYLDDFHVESIDTARIIFNQVMEKEFEDGIINWGRIVTIFAFGGVLLKKLKQEQIALDVSAYKQVSSFVAEFIMNNTGEWIRQNGGWEDGFIKKFE 149
                                     8        18     |   -  |     38        48        58        68        78        88        98       108       118       128       138       148 
                                                    24     31                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:22
 aligned with BMF_MOUSE | Q91ZE9 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:22
                                   138       148  
            BMF_MOUSE   129 RAEVQIARKLQCIADQFHRLHT 150
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 2vog B 129 RAEVQIARKLQCIADQFHRLHT 150
                                   138       148
   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
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Bcl-2] (60)

(-) Gene Ontology  (24, 28)

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   (BMF_MOUSE | Q91ZE9)
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).
biological process
    GO:0043276    anoikis    Apoptosis triggered by inadequate or inappropriate adherence to substrate e.g. after disruption of the interactions between normal epithelial cells and the extracellular matrix.
    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:2001234    negative regulation of apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of 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:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of 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: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.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016459    myosin complex    A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

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  B2LA1_MOUSE | Q07440
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  BMF_MOUSE | Q91ZE9
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 Related Entries

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

UniProtKB/Swiss-Prot
        B2LA1_MOUSE | Q07440: 2vof 2voh 2voi

(-) Related Entries Specified in the PDB File

2vof STRUCTURE OF MOUSE A1 BOUND TO THE PUMA BH3-DOMAIN
2voh STRUCTURE OF MOUSE A1 BOUND TO THE BAK BH3-DOMAIN
2voi STRUCTURE OF MOUSE A1 BOUND TO THE BID BH3-DOMAIN