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(-) Description

Title :  CRYSTAL STRUCTURE OF LIGHT MUTANT
 
Authors :  W. Liu, C. Zhan, P. R. Kumar, J. B. Bonanno, S. G. Nathenson, S. C. Almo, Ne Structural Genomics Research Consortium (Nysgrc), Atoms-To-A The Immune Function Network (Ifn)
Date :  28 Apr 13  (Deposition) - 07 Aug 13  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
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, Jelly-Roll Fold, Bind Tnf Receptor Hvem And Ltbr, Ltbr, Protein Structure Initiative, Ifn (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: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TNFSF14, HVEML, LIGHT, UNQ391/PRO726
    Mutation: YES
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4KG8)

(-) Sites  (0, 0)

(no "Site" information available for 4KG8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KG8)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:220 -Asp A:221
2Arg A:223 -Leu A:224
3Ser B:103 -Ser B:104
4Gly B:107 -Ser B:108
5Gly B:109 -Gly B:110
6Gln C:117 -Leu C:118
7Leu C:118 -Gly C:119
8Asn C:196 -Trp C:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KG8)

(-) Exons   (0, 0)

(no "Exon" information available for 4KG8)

(-) 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:129
                                                                                                                                                                 
               SCOP domains d4kg8a_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..........eee......eee.eeee..eeee...eeeeeeeeeeeee...eeeeeeee.......eeeeeeee....eeeeeeeeeeeee....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kg8 A  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGTITHGLYKRTPRYPEELELLVSQQSPSNWFDSSFLGGVVHLEAGEEVVVRVLDERLGTRSYFGAFMV 240
                                   101       111       121       131       141       151 ||    168       178       196       206       216       231         
                                                                                       153|                      186|                          224|          
                                                                                        161                       195                           230          


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4kg8b_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...........ee......eee..eee..eee....eeeeeeeeeee....eeeeeeee.....eeeeeeee.....eeeeeeeeeee....eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kg8 B  93 NPAAHLTGANSSGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGASTITHGLYKRTYPEELELLVSQQSPNWFDSSFLGGVVHLEAGEEVVVRVLDEGTRSYFGAFMV 240
                                   102 ||    114       124       134       144     ||162       174       184 ||    203       213       230       240
                                     104|                                        150|        170|          186|                       222|          
                                      107                                         159         173           196                        230          


Chain C from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.............eee.eeee..eeee...eeeeeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeeeeeeeee....eeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4kg8 C  93 NPAAHLTGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVASTITHGLYKRTPRYPEELELLVSQQSPNWFDSSFLGGVVHLEAGEEVVVRVLDTRSYFGAFMV 240
                                   111       121       131       141       151||     167       177       196       206       216    || 235     
                                 100|                                       152|                        186|                      221|         
                                  110                                        159                         196                       231
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KG8)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4kg8)
 
  Cis Peptide Bonds
    Arg A:223 - Leu A:224   [ RasMol ]  
    Asn C:196 - Trp C:197   [ RasMol ]  
    Gln C:117 - Leu C:118   [ RasMol ]  
    Gly B:107 - Ser B:108   [ RasMol ]  
    Gly B:109 - Gly B:110   [ RasMol ]  
    Leu A:220 - Asp A:221   [ RasMol ]  
    Leu C:118 - Gly C:119   [ RasMol ]  
    Ser B:103 - Ser B:104   [ RasMol ]  
 

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  4kg8
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  TNF14_HUMAN | O43557
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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF14_HUMAN | O43557: 4en0 4j6g 4kgg 4kgq 4rsu

(-) Related Entries Specified in the PDB File

3k51
3mhd RELATED ID: NYSGRC-011104 RELATED DB: TARGETTRACK
3mi8
4en0
4fhq
4j6g