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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN LIGHT LOOP MUTANT IN COMPLEX WITH DCR3
 
Authors :  W. Liu, C. Zhan, J. B. Bonanno, P. Sampathkumar, R. Toro, S. G. Nathenson S. C. Almo, New York Structural Genomics Research Consortium ( Atoms-To-Animals: The Immune Function Network (Ifn)
Date :  29 Apr 13  (Deposition) - 10 Jul 13  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Light, Dcr3, Tnf, Tnfr, Tnf14, Structural Genomics, Psi-Biology, New Hvem, N-Glycosylation, Membrane, Secreted Protein, Cytokine, Ifn, Jelly-Roll Fold, Bind Tnf Receptor Hvem And Ltbr, Ltbr, Protein Structure Initiative, Atoms-To-Animals: The Immune Function Network, New York Structural Genomics Research Consortium, Nysgrc, Immune System (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 RECEPTOR SUPERFAMILY MEMBER 6B
    Chains: C, D
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Taxid: 7215
    Fragment: UNP RESIDUES 30-195
    Gene: TNFRSF6B, DCR3, TR6, UNQ186/PRO212
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DECOY RECEPTOR 3, DCR3, DECOY RECEPTOR FOR FAS LIGAND, M68
 
Molecule 2 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21-PHYS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 83-240
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3MG2Ligand/IonMAGNESIUM ION
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:132 , PRO C:133 , ALA C:136 , SER C:159 , SER C:161 , HOH C:401BINDING SITE FOR RESIDUE MG C 301
2AC2SOFTWARECYS D:132 , PRO D:133 , ALA D:136 , SER D:159 , SER D:161 , HOH D:402BINDING SITE FOR RESIDUE MG D 301
3AC3SOFTWAREASN C:173 , GLN D:80 , PHE D:81 , TRP D:82 , ARG D:103 , HIS D:106 , THR D:108 , HIS D:109BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 173 RESIDUES 302 TO 305
4AC4SOFTWAREPRO C:54 , TRP C:82 , ASN D:173 , THR D:175 , ALA D:176BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 173 RESIDUES 302 TO 303

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:154 -A:187
2B:154 -B:187
3C:49 -C:62
4C:52 -C:70
5C:73 -C:88
6C:91 -C:105
7C:95 -C:113
8C:115 -C:126
9C:132 -C:150
10C:153 -C:168
11C:174 -C:193
12D:49 -D:62
13D:52 -D:70
14D:73 -D:88
15D:91 -D:105
16D:95 -D:113
17D:115 -D:126
18D:132 -D:150
19D:153 -D:168
20D:174 -D:193

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:220 -Asp A:221
2Leu B:220 -Asp B:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KGQ)

(-) 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:139
                                                                                                                                                                           
               SCOP domains d4kgqa_ A: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......................eee..eee..eee....eeeeeeeeeeeeee.....eeeeeeee.......eeeeeeee.....eeeeeeeeeeeeee....eeeeeeehhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgq A  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCASTITHGLYKRTPRYPEELELLVSQQSPCGRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVDYTKEDRSYFGAFMV 240
                                   101       111       121       131       141       151  ||   165       175       185  ||   201       211       221       231         
                                                                                        154|                          188|                                             
                                                                                         159                           195                                             


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains d4kgqb_ B: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......................eee..eee..eee....eeeeeeeeeeeeee.....eeeeeeee.......eeeeeeee.....eeeeeeeeeeeeee....eeeeeeehhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgq B  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCASTITHGLYKRTPRYPEELELLVSQQSPCGRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVDYTKEDRSYFGAFMV 240
                                   101       111       121       131       141       151  ||   165       175       185  ||   201       211       221       231         
                                                                                        154|                          188|                                             
                                                                                         159                           195                                             


Chain C from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.....eeeee........eeee....ee..........ee........eeeee........eeee...eeee..eeee.......eeeee........eeee....ee..........ee..hhhhhh..eee........ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgq C  33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQCQPHRNCTALGLALNVPGSSSHDTLCTSTGHH 199
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain D from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......eeeee.....eeeee........eeee....ee..........ee........eeeee........eeee...eeee..eeee.......eeeee........eeee....ee..........ee.........eeee........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgq D  32 ETPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQCQPHRNCTALGLALNVPGSSSHDTLCTS 195
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 41)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF14_HUMAN | O43557: 4en0 4j6g 4kg8 4kgg 4rsu
        TNF6B_HUMAN | O95407: 3k51 3mhd 3mi8 4j6g 4kgg 4msv 5l36

(-) Related Entries Specified in the PDB File

3k51
3mhd
3mi8
4en0
4j6g RELATED ID: NYSGRC-011104 RELATED DB: TARGETTRACK RELATED ID: NYSGRC-011073 RELATED DB: TARGETTRACK