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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNC5H2 DEATH DOMAIN
 
Authors :  N. Handa, K. Murayama, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Jul 04  (Deposition) - 09 Jan 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Six Helix Bundle, Death Domain, Apoptosis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Handa, M. Kukimoto-Niino, R. Akasaka, K. Murayama, T. Terada, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, A. Tanaka, Y. Hayashizaki, T. Kigawa, M. Shirouzu, S. Yokoyama
Structure Of The Unc5H2 Death Domain
Acta Crystallogr. , Sect. D V. 62 1502 2006
PubMed-ID: 17139086  |  Reference-DOI: 10.1107/S0907444906039369

(-) Compounds

Molecule 1 - NETRIN RECEPTOR UNC5H2
    ChainsA, B, C, D, E, F
    EngineeredYES
    FragmentDEATH DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric/Biological Unit (3, 34)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2SO37Ligand/IonSULFITE ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:4 , HOH A:166 , ARG A:876 , LYS B:932 , GLU B:934 , MSE B:935BINDING SITE FOR RESIDUE SO3 A 1001
02AC2SOFTWAREASN D:874 , ARG D:876 , ASN D:878 , LYS D:932BINDING SITE FOR RESIDUE SO3 D 1002
03AC3SOFTWAREASN C:874 , ASN C:878BINDING SITE FOR RESIDUE SO3 C 1003
04AC4SOFTWARESER C:888 , MSE C:889 , ASP C:890 , ARG C:891BINDING SITE FOR RESIDUE SO3 C 1004
05AC5SOFTWARESER E:888 , MSE E:889 , ASP E:890 , ARG E:891BINDING SITE FOR RESIDUE SO3 E 1005
06AC6SOFTWAREHOH D:54 , SER D:869 , LYS D:932 , GLU D:934BINDING SITE FOR RESIDUE SO3 D 1006
07AC7SOFTWARELYS C:865 , HOH E:147 , PRO E:859 , LEU E:860 , SER E:861BINDING SITE FOR RESIDUE SO3 E 1007
08AC8SOFTWARETRP E:910 , ARG E:913 , GLN E:914 , SER E:922BINDING SITE FOR RESIDUE SO4 E 2001
09AC9SOFTWARETRP F:910 , ARG F:913 , GLN F:914 , SER F:922BINDING SITE FOR RESIDUE SO4 F 2002
10BC1SOFTWARETRP C:910 , ARG C:913 , GLN C:914 , SER C:922BINDING SITE FOR RESIDUE SO4 C 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WMG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WMG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WMG)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEATH_DOMAINPS50017 Death domain profile.UNC5B_MOUSE877-943
 
 
 
 
 
  6A:877-943
B:877-941
C:877-942
D:877-942
E:877-941
F:877-941

(-) Exons   (0, 0)

(no "Exon" information available for 1WMG)

(-) 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:90
 aligned with UNC5B_MOUSE | Q8K1S3 from UniProtKB/Swiss-Prot  Length:945

    Alignment length:90
                                   863       873       883       893       903       913       923       933       943
          UNC5B_MOUSE   854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEMGKSEMLVAMATDG 943
               SCOP domains d1wmga_ A: Netrin receptor UNC5B                                                           SCOP domains
               CATH domains 1wmgA00 A:854-943 Death Domain, Fas                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------DEATH_DOMAIN  PDB: A:877-943 UniProt: 877-943                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1wmg A 854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSmDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEmGKSEmLVAmATDG 943
                                   863       873       883     | 893       903       913       923      |933 |   | 943
                                                             889-MSE                                  930-MSE|   |    
                                                                                                           935-MSE    
                                                                                                               939-MSE

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with UNC5B_MOUSE | Q8K1S3 from UniProtKB/Swiss-Prot  Length:945

    Alignment length:87
                                   864       874       884       894       904       914       924       934       
          UNC5B_MOUSE   855 AFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEMGKSEMLVAMAT 941
               SCOP domains d1wmgb_ B: Netrin receptor UNC5B                                                        SCOP domains
               CATH domains 1wmgB00 B:855-941 Death Domain, Fas                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh.----hhhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------DEATH_DOMAIN  PDB: B:877-941 UniProt: 877-943                     PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1wmg B 855 AFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSmDRYLNYFATKASPTGVILDLWEARQ----DLNSLASALEEmGKSEmLVAmAT 941
                                   864       874       884    |  894       904       914    |  924     | 934|   |  
                                                            889-MSE                  914  919        930-MSE|   |  
                                                                                                          935-MSE  
                                                                                                              939-MSE

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with UNC5B_MOUSE | Q8K1S3 from UniProtKB/Swiss-Prot  Length:945

    Alignment length:89
                                   863       873       883       893       903       913       923       933         
          UNC5B_MOUSE   854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEMGKSEMLVAMATD 942
               SCOP domains d1wmgc_ C: Netrin receptor UNC5B                                                          SCOP domains
               CATH domains 1wmgC00 C:854-942 Death Domain, Fas                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh......hhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh...-..hhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DEATH_DOMAIN  PDB: C:877-942 UniProt: 877-943                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1wmg C 854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSmDRYLNYFATKASPTGVILDLWEARQQD-GDLNSLASALEEmGKSEmLVAmATD 942
                                   863       873       883     | 893       903       913  | |  923      |933 |   |   
                                                             889-MSE                    916 |         930-MSE|   |   
                                                                                          918              935-MSE   
                                                                                                               939-MSE

Chain D from PDB  Type:PROTEIN  Length:86
 aligned with UNC5B_MOUSE | Q8K1S3 from UniProtKB/Swiss-Prot  Length:945

    Alignment length:89
                                   863       873       883       893       903       913       923       933         
          UNC5B_MOUSE   854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEMGKSEMLVAMATD 942
               SCOP domains d1wmgd_ D: Netrin receptor UNC5B                                                          SCOP domains
               CATH domains 1wmgD00 D:854-942 Death Domain, Fas                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh......hhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhh.---..hhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DEATH_DOMAIN  PDB: D:877-942 UniProt: 877-943                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1wmg D 854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSmDRYLNYFATKASPTGVILDLWEARQ---GDLNSLASALEEmGKSEmLVAmATD 942
                                   863       873       883     | 893       903       913|   |  923      |933 |   |   
                                                             889-MSE                  914 918         930-MSE|   |   
                                                                                                           935-MSE   
                                                                                                               939-MSE

Chain E from PDB  Type:PROTEIN  Length:88
 aligned with UNC5B_MOUSE | Q8K1S3 from UniProtKB/Swiss-Prot  Length:945

    Alignment length:88
                                   863       873       883       893       903       913       923       933        
          UNC5B_MOUSE   854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEMGKSEMLVAMAT 941
               SCOP domains d1wmge_ E: Netrin receptor UNC5B                                                         SCOP domains
               CATH domains 1wmgE00 E:854-941 Death Domain, Fas                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh......hhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DEATH_DOMAIN  PDB: E:877-941 UniProt: 877-943                     PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1wmg E 854 YAFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSmDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEmGKSEmLVAmAT 941
                                   863       873       883     | 893       903       913       923      |933 |   |  
                                                             889-MSE                                  930-MSE|   |  
                                                                                                           935-MSE  
                                                                                                               939-MSE

Chain F from PDB  Type:PROTEIN  Length:87
 aligned with UNC5B_MOUSE | Q8K1S3 from UniProtKB/Swiss-Prot  Length:945

    Alignment length:87
                                   864       874       884       894       904       914       924       934       
          UNC5B_MOUSE   855 AFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEMGKSEMLVAMAT 941
               SCOP domains d1wmgf_ F: Netrin receptor UNC5B                                                        SCOP domains
               CATH domains 1wmgF00 F:855-941 Death Domain, Fas                                                     CATH domains
           Pfam domains (1) ---------Death-1wmgF01 F:864-941                                                        Pfam domains (1)
           Pfam domains (2) ---------Death-1wmgF02 F:864-941                                                        Pfam domains (2)
           Pfam domains (3) ---------Death-1wmgF03 F:864-941                                                        Pfam domains (3)
           Pfam domains (4) ---------Death-1wmgF04 F:864-941                                                        Pfam domains (4)
           Pfam domains (5) ---------Death-1wmgF05 F:864-941                                                        Pfam domains (5)
           Pfam domains (6) ---------Death-1wmgF06 F:864-941                                                        Pfam domains (6)
         Sec.struct. author ....hhhhhhhhhhhhh.......hhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------DEATH_DOMAIN  PDB: F:877-941 UniProt: 877-943                     PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1wmg F 855 AFKIPLSIRQKICSSLDAPNSRGNDWRLLAQKLSmDRYLNYFATKASPTGVILDLWEARQQDDGDLNSLASALEEmGKSEmLVAmAT 941
                                   864       874       884    |  894       904       914       924     | 934|   |  
                                                            889-MSE                                  930-MSE|   |  
                                                                                                          935-MSE  
                                                                                                              939-MSE

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Death (18)
(-)
Family: Death (11)
1aDeath-1wmgF01F:864-941
1bDeath-1wmgF02F:864-941
1cDeath-1wmgF03F:864-941
1dDeath-1wmgF04F:864-941
1eDeath-1wmgF05F:864-941
1fDeath-1wmgF06F:864-941

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (UNC5B_MOUSE | Q8K1S3)
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:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0033564    anterior/posterior axon guidance    The process in which the migration of an axon growth cone is directed to a specific target site along the anterior-posterior body axis in response to a combination of attractive and repulsive cues. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    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:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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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