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(-) Description

Title :  HUMAN BIR2 DOMAIN OF BACULOVIRAL INHIBITOR OF APOPTOSIS REPEAT-CONTAINING 1 (BIRC1)
 
Authors :  M. D. Herman, M. Welin, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, M. Moche, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, P. Nordlund, Structural Genomics Consortium (Sgc)
Date :  23 Jan 08  (Deposition) - 29 Jan 08  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. D. Herman, M. Moche, S. Flodin, M. Welin, L. Tresaugues, I. Johansson, M. E. Nilsson, P. Nordlund, T. Nyman
Structures Of Bir Domains From Human Naip And Ciap2.
Acta Crystallogr. , Sect. F V. 65 1091 2009
PubMed-ID: 19923725  |  Reference-DOI: 10.1107/S1744309109038597

(-) Compounds

Molecule 1 - BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3) R3 PRARE
    Expression System Taxid469008
    FragmentBIR2 DOMAIN, RESIDUES 141-244
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBACULOVIRAL INHIBITOR OF APOPTOSIS REPEAT-CONTAINING 1, NEURONAL APOPTOSIS INHIBITORY PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:197 , CYS A:200 , HIS A:217 , CYS A:224BINDING SITE FOR RESIDUE ZN A1245
2AC2SOFTWAREGLY A:175 , ILE A:176 , SER A:177 , GLN A:192 , ASP A:211 , HOH A:2026 , HOH A:2050 , HOH A:2051BINDING SITE FOR RESIDUE GOL A1246

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VM5)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIR_REPEAT_1PS01282 BIR repeat.BIRC1_HUMAN60-127
159-227
278-345
  1-
A:159-227
-
2BIR_REPEAT_2PS50143 BIR repeat profile.BIRC1_HUMAN63-128
162-228
281-346
  1-
A:162-228
-

(-) Exons   (0, 0)

(no "Exon" information available for 2VM5)

(-) 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:103
 aligned with BIRC1_HUMAN | Q13075 from UniProtKB/Swiss-Prot  Length:1403

    Alignment length:106
                                   148       158       168       178       188       198       208       218       228       238      
          BIRC1_HUMAN   139 DIRVKNLKSRLRGGKMRYQEEEARLASFRNWPFYVQGISPCVLSEAGFVFTGKQDTVQCFSCGGCLGNWEEGDDPWKEHAKWFPKCEFLRSKKSSEEITQYIQSYK 244
               SCOP domains d2vm5a_ A: a   utomated matches                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------BIR-2vm5A01 A:162-228                                              ---------------- Pfam domains
         Sec.struct. author .ee.........---....hhhhhhhhhhhhhhhhh..hhhhhhhh.eee......eee.....eee......hhhhhhhhhh..hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------BIR_REPEAT_1  PDB: A:159-227 UniProt: 159-227                        ----------------- PROSITE (1)
                PROSITE (2) -----------------------BIR_REPEAT_2  PDB: A:162-228 UniProt: 162-228                      ---------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2vm5 A 139 SMRVKNLKSRLR---MRYQEEEARLASFRNWPFYVQGISPCVLSEAGFVFTGKQDTVQCFSCGGCLGNWEEGDDPWKEHAKWFPKCEFLRSKKSSEEITQYIQSYK 244
                                   148 |   | 158       168       178       188       198       208       218       228       238      
                                     150 154                                                                                          

   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 2VM5)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: BIR-like (25)
(-)
Family: BIR (25)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BIRC1_HUMAN | Q13075)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
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:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0009966    regulation of signal transduction    Any process that modulates the frequency, rate or extent of signal transduction.
    GO:0043200    response to amino acid    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 amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0048678    response to axon injury    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 axon injury stimulus.
cellular component
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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