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(-) Description

Title :  CRYSTAL STRUCTURE OF LIGHT
 
Authors :  C. Zhan, W. Liu, Y. Patskovsky, U. A. Ramagopal, J. B. Bonanno, S. G. Nath S. C. Almo, New York Structural Genomics Research Consortium ( Atoms-To-Animals: The Immune Function Network (Ifn)
Date :  12 Apr 12  (Deposition) - 09 May 12  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Immunity, Tnf Superfamily, Hvem, Dcr3, N-Glycosylation, Membrane, Secreted Protein, Cytokine, Atoms-To- Animals: The Immune Function Network, Ifn, Jelly-Roll Fold, Bind Tnf Receptor Hvem And Ltbr, Ltbr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Liu, C. Zhan, H. Cheng, P. R. Kumar, J. B. Bonanno, S. G. Nathenson, S. C. Almo
Mechanistic Basis For Functional Promiscuity In The Tnf And Tnf Receptor Superfamilies: Structure Of The Light:Dcr3 Assembly.
Structure V. 22 1252 2014
PubMed-ID: 25087510  |  Reference-DOI: 10.1016/J.STR.2014.06.013

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14
    Chains: A, B, C
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Plasmid: PMT/BIP/V5-HIS
    Expression System Taxid: 7215
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN
    Gene: HVEML, LIGHT, TNFSF14, UNQ391/PRO726
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HERPES VIRUS ENTRY MEDIATOR LIGAND, HVEM-L, HERPESVIRUS ENTRY MEDIATOR LIGAND, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14, SOLUBLE FORM

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:139 , TYR A:140 , MET A:239 , VAL A:240 , ARG B:124BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREGLN A:184 , SER A:200 , SER A:201 , PHE A:202 , GLN B:184 , SER B:200 , GLN C:184 , SER C:200BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREASN A:102 , SER A:104 , LEU A:118 , GLY A:119BINDING SITE FOR RESIDUE NAG A 303

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:154 -A:187
2B:154 -B:187
3C:154 -C:187

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EN0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EN0)

(-) Exons   (0, 0)

(no "Exon" information available for 4EN0)

(-) 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
                                                                                                                                                                                 
               SCOP domains d4en0a_ A: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhh...eee......eee.eeee..eeee...eeeeeeeeeeeee..........eeeeeeee......eeeeeeeeehhhhhh...eeeeeeeeeeeee....eeeeeee.......hhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en0 A  93 NPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCPLGLASTITHGLYKRTPRYPEELELLVSQQSPCGRATRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 240
                                   102       112       122       132       142       152       162       172       182       195       205       215       225       235     
                                                                                                                            191|                                             
                                                                                                                             195                                             


Chain B from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains d4en0b_ B: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..........ee......ee...eee..eee....eeeeeeeeeeeeee......eeeeeeee.......eeeeeeee...........eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en0 B  92 VNPAAHLTGANSSSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCPLSTITHGLYKRTPRYPEELELLVSQQSPCGRATSSSRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 240
                                   101  ||   114       124       134       144       154 ||    167       177       187       197       207       217       227       237   
                                      104|                                             156|                                                                                
                                       108                                              160                                                                                


Chain C from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains d4en0c_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..................ee..eeee..eeee...eeeeeeeeeeeee....hhhhh.eeeeeeeee....eeeeeeeeee............eeeeeeeeeeeee....eeeeee..............eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4en0 C  92 VNPAAHLTGANSSGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCPLGLASTITHGLYKRTPRYPEELELLVSQQSPCGRATSSSRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 240
                                   101  ||   116       126       136       146       156       166       176       186       196       206       216       226       236    
                                      104|                                                                                                                                  
                                       110
   Legend:   → Mismatch (orange background)
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  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, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EN0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EN0)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        TNF14_HUMAN | O43557: 4j6g 4kg8 4kgg 4kgq 4rsu

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