4J6G - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LIGHT AND DCR3 COMPLEX

Authors :   W. Liu, C. Zhan, J. B. Bonanno, R. C. Bhosle, S. G. Nathenson, S. C. Almo, A Animals: The Immune Function Network (Ifn), New York Structu Genomics Research Consortium (Nysgrc)

Date :   11 Feb 13 (Deposition) - 13 Mar 13 (Release) - 31 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A (3x),B (3x),C (3x),D (3x)
Biol. Unit 2: A,C  (3x)
Biol. Unit 3: B,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

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	DROSOPHILA
	Expression System Taxid	:	7215
	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

Molecule 2 - 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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A (3x)	B (3x)	C (3x)	D (3x)
Biological Unit 2 (3x)	:	A		C
Biological Unit 3 (3x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:228 , ASP A:229 , GLY A:230 , ARG A:232 , SER A:233 , HOH A:404	BINDING SITE FOR RESIDUE CL A 301
2	AC2	SOFTWARE	ARG B:228 , ASP B:229 , GLY B:230 , ARG B:232 , SER B:233	BINDING SITE FOR RESIDUE CL B 301
3	AC3	SOFTWARE	ASN C:173 , THR C:175 , NAG C:302 , HOH C:701 , PHE D:81	BINDING SITE FOR RESIDUE NAG C 301
4	AC4	SOFTWARE	NAG C:301 , BMA C:303 , PRO D:54 , GLN D:80 , TRP D:82	BINDING SITE FOR RESIDUE NAG C 302
5	AC5	SOFTWARE	NAG C:302 , MAN C:304 , HIS D:106 , THR D:108	BINDING SITE FOR RESIDUE BMA C 303
6	AC6	SOFTWARE	BMA C:303 , ARG D:103 , HIS D:109	BINDING SITE FOR RESIDUE MAN C 304
7	AC7	SOFTWARE	CYS C:132 , PRO C:133 , ALA C:136 , SER C:159 , SER C:161 , HOH C:707	BINDING SITE FOR RESIDUE MG C 305
8	AC8	SOFTWARE	TRP C:82 , ASN D:173	BINDING SITE FOR RESIDUE NAG D 301
9	AC9	SOFTWARE	CYS D:132 , PRO D:133 , ALA D:136 , SER D:159 , SER D:161 , HOH D:406	BINDING SITE FOR RESIDUE MG D 302

Asymmetric Unit

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

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4J6G)

(no "PROSITE Motif" information available for 4J6G)

(no "Exon" information available for 4J6G)

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 d4j6ga_ A: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......................eee.eeee..eeee...eeeeeeeeeeeeee.....eeeeeeee.......eeeeeeee.....eeeeeeeeeeeeee....eeeeeeehhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6g A  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCASTITHGLYKRTPRYPEELELLVSQQSPCGRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 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 d4j6gb_ 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
                 4j6g B  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCASTITHGLYKRTPRYPEELELLVSQQSPCGRVWWDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 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:163
                                                                                                                                                                                                   
               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..........eee........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6g C  33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQCQPHRNCTALGLALNVPGSSSHDTLCTS 195
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain D from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               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...hhhhh..eee........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j6g D  33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQCQPHRNCTALGLALNVPGSSSHDTLCT 194
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: TNF-like (100)

Superfamily: TNF-like (100)

Family: automated matches (18)

Protein domain: automated matches (18)

Human (Homo sapiens) [TaxId: 9606] (18)

1a	d4j6ga_	A:
1b	d4j6gb_	B:

(no "CATH Domain" information available for 4J6G)

(no "Pfam Domain" information available for 4J6G)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Leu A:220 - Asp A:221	[ RasMol ]
		Leu B:220 - Asp B:221	[ RasMol ]

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

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

SS Bonds (20, 20)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (35, 41)

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Related Entries Specified in the PDB File