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(-) Description

Title :  CED-2
 
Authors :  Y. Kang, J. Sun, Y. Liu, D. Sun, Y. Hu, Y. F. Liu
Date :  28 Feb 11  (Deposition) - 08 Jun 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Engulfment, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kang, J. Xu, Y. Liu, J. Sun, D. Sun, Y. Hu, Y. Liu
Crystal Structure Of The Cell Corpse Engulfment Protein Ced-2 In Caenorhabditis Elegans.
Biochem. Biophys. Res. Commun. V. 410 189 2011
PubMed-ID: 21616056  |  Reference-DOI: 10.1016/J.BBRC.2011.05.051

(-) Compounds

Molecule 1 - CELL DEATH ABNORMALITY PROTEIN 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCED-2, Y41D4B.13
    Organism CommonNEMATODE
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymCELL-CORPSE ENGULFMENT PROTEIN CED-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , ARG A:41 , SER A:43 , SER A:44 , SER A:50BINDING SITE FOR RESIDUE SO4 A 280
2AC2SOFTWAREARG B:21 , ARG B:41 , SER B:43 , SER B:44 , SER B:50BINDING SITE FOR RESIDUE GOL B 280

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QWY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QWY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QWY)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.CED2_CAEEL14-117
 
  2A:14-117
B:14-117
2SH3PS50002 Src homology 3 (SH3) domain profile.CED2_CAEEL116-176
 
  2A:116-174
B:116-174
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.CED2_CAEEL14-117
 
  1A:14-117
-
2SH3PS50002 Src homology 3 (SH3) domain profile.CED2_CAEEL116-176
 
  1A:116-174
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.CED2_CAEEL14-117
 
  1-
B:14-117
2SH3PS50002 Src homology 3 (SH3) domain profile.CED2_CAEEL116-176
 
  1-
B:116-174

(-) Exons   (0, 0)

(no "Exon" information available for 3QWY)

(-) Sequences/Alignments

Asymmetric 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:170
 aligned with CED2_CAEEL | Q9NHC3 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
           CED2_CAEEL     5 GFDPFEWRSFYFPGMSREEAHKLLGEPQVSIGTFLMRDSSRPGEYSLTVREADEGNAVCHYLIERGEPKEDGTAAAGVKIANQSFPDIPALLNHFKMRVLTEASLLAAYKKPIIEVVVGTFKFTGERETDLPFEQGERLEILSKTNQDWWEARNALGTTGLVPANYVQIQ 174
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.ee...hhhhhhhhhhh......eeeeee......eeeeee.......eeeeeeee............eee..eee.hhhhhhhhhhhh........ee......eeeee..................eeeeee.....eeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------SH2  PDB: A:14-117 UniProt: 14-117                                                                      --------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------SH3  PDB: A:116-174 UniProt: 116-176                        PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qwy A   5 GFDPFEWRSFYFPGMSREEAHKLLGEPQVSIGTFLMRDSSRPGEYSLTVREADEGNAVCHYLIERGEPKEDGTAAAGVKIANQSFPDIPALLNHFKMRVLTEASLLAAYKKPIIEVVVGTFKFTGERETDLPFEQGERLEILSKTNQDWWEARNALGTTGLVPANYVQIQ 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with CED2_CAEEL | Q9NHC3 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
           CED2_CAEEL     5 GFDPFEWRSFYFPGMSREEAHKLLGEPQVSIGTFLMRDSSRPGEYSLTVREADEGNAVCHYLIERGEPKEDGTAAAGVKIANQSFPDIPALLNHFKMRVLTEASLLAAYKKPIIEVVVGTFKFTGERETDLPFEQGERLEILSKTNQDWWEARNALGTTGLVPANYVQIQ 174
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------SH2-3qwyB03 B:14-99                                                                   ----------------------SH3_1-3qwyB01 B:122-168                        ------ Pfam domains (1)
           Pfam domains (2) ---------SH2-3qwyB04 B:14-99                                                                   ----------------------SH3_1-3qwyB02 B:122-168                        ------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh......hhhhhhh........eeeeee......eeeeee.......eeeeeeee............eee..eee.hhhhhhhhhhhh........ee......eeeee..................eeeeeeeee..eeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------SH2  PDB: B:14-117 UniProt: 14-117                                                                      --------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------SH3  PDB: B:116-174 UniProt: 116-176                        PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qwy B   5 GFDPFEWRSFYFPGMSREEAHKLLGEPQVSIGTFLMRDSSRPGEYSLTVREADEGNAVCHYLIERGEPKEDGTAAAGVKIANQSFPDIPALLNHFKMRVLTEASLLAAYKKPIIEVVVGTFKFTGERETDLPFEQGERLEILSKTNQDWWEARNALGTTGLVPANYVQIQ 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

   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 3QWY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QWY)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CED2_CAEEL | Q9NHC3)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    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).
biological process
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0043652    engulfment of apoptotic cell    The removal of the apoptotic cell by phagocytosis, by a neighboring cell or by a phagocyte.
    GO:0006909    phagocytosis    An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

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 Related Entries

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

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        CED2_CAEEL | Q9NHC33qwx

(-) Related Entries Specified in the PDB File

3qwx