1XU1 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF APRIL BOUND TO TACI

Authors :   S. G. Hymowitz, D. R. Patel, H. J. A. Wallweber, S. Runyon, M. Yan, J. Yin, S. K. Shriver, N. C. Gordon, B. Pan, N. J. Skelton, R. F. Kelley, M. A. Sta

Date :   25 Oct 04 (Deposition) - 09 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,D,R,S,T

Keywords :   Tnfsf, Cytokine, Crd, Receptor, Jelly-Roll, Cysteine-Rich, Hormone- Growth Factor Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. G. Hymowitz, D. R. Patel, H. J. A. Wallweber, S. Runyon, M. Yan, J. Yin S. K. Shriver, N. C. Gordon, B. Pan, N. J. Skelton, R. F. Kelley, M. A. Starovasnik
Structures Of April-Receptor Complexes: Like Bcma, Taci Employs Only A Single Cysteine-Rich Domain For High-Affinit Ligand Binding
J. Biol. Chem. V. 280 7218 2005
PubMed-ID: 15542592 | Reference-DOI: 10.1074/JBC.M411714200

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13
	Chains	:	A, B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-32A (MODIFIED)
	Expression System Strain	:	ORIGAMI (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TNF DOMAIN OF MURINE APRIL
	Gene	:	TNFSF13, APRIL
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	A PROLIFERATION-INDUCING LIGAND, APRIL, TNFSF13, TALL-2

Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 13B
	Chains	:	R, S, T
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A (MODIFIED)
	Expression System Strain	:	ORIGAMI (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TACI CRD2
	Gene	:	TNFRSF13B, TACI
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRANSMEMBRANE ACTIVATOR AND CAML INTERACTOR, TNFRSF13B

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	D	R	S	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:106 , HOH A:242 , HIS B:106 , HIS D:106 , HOH D:253 , HOH D:281	BINDING SITE FOR RESIDUE NI A 101

Asymmetric/Biological Unit

No.	Residues
1	A:187	-	A:202
2	B:187	-	B:202
3	D:187	-	D:202
4	R:71	-	R:86
5	R:89	-	R:100
6	R:93	-	R:104
7	S:71	-	S:86
8	S:89	-	S:100
9	S:93	-	S:104
10	T:71	-	T:86
11	T:89	-	T:100
12	T:93	-	T:104

(no "Cis Peptide Bond" information available for 1XU1)

Asymmetric/Biological Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024027	C	104	R	TR13B_HUMAN	Disease (IGAD2)	34557412	R/S/T	C	104	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	TNF13_MOUSE	108-241	3	A:108-241 B:108-241 D:108-241
2	TNF_1	PS00251	TNF family signature.	TNF13_MOUSE	146-162	3	A:146-162 B:146-162 D:146-162

Asymmetric/Biological Unit (1, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000261652	1	ENSE00001378434	chr17:16875402-16875329	74	TR13B_HUMAN	1-21	21	0	-	-
1.2	ENST00000261652	2	ENSE00001309090	chr17:16855897-16855760	138	TR13B_HUMAN	21-67	47	0	-	-
1.3	ENST00000261652	3	ENSE00001151854	chr17:16852297-16852052	246	TR13B_HUMAN	67-149	83	3	R:68-105 S:71-106 T:71-109	38 36 39
1.4	ENST00000261652	4	ENSE00000691547	chr17:16843825-16843640	186	TR13B_HUMAN	149-211	63	0	-	-
1.5b	ENST00000261652	5b	ENSE00001323387	chr17:16843111-16842399	713	TR13B_HUMAN	211-293	83	0	-	-

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:137
 aligned with TNF13_MOUSE | Q9D777 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:137
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       
          TNF13_MOUSE   105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
               SCOP domains d1xu1a_ A: A proliferation-inducing ligand, APRIL                                                                                         SCOP domains
               CATH domains 1xu1A00 A:105-241  [code=2.60.120.40, no name defined]                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.......eeeeeeeeeee...eeee..eeee...eeeeeeeeeeee....eeeeeeeeee..eeeeeeeeeee........eeeeeeeeeeee....eeeeee..............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TNF_2  PDB: A:108-241 UniProt: 108-241                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------TNF_1            ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xu1 A 105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
                                   114       124       134       144       154       164       174       184       194       204       214       224       234

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with TNF13_MOUSE | Q9D777 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:137
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       
          TNF13_MOUSE   105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
               SCOP domains d1xu1b_ B: A proliferation-inducing ligand, APRIL                                                                                         SCOP domains
               CATH domains 1xu1B00 B:105-241  [code=2.60.120.40, no name defined]                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.......eeeeeeeeeee...eeee..eeee...eeeeeeeeeeee....eeeeeeeeee..eeeeeeeeeee...hhhh.eeeeeeeeeeee....eeeeee..............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TNF_2  PDB: B:108-241 UniProt: 108-241                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------TNF_1            ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xu1 B 105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
                                   114       124       134       144       154       164       174       184       194       204       214       224       234

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with TNF13_MOUSE | Q9D777 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:137
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       
          TNF13_MOUSE   105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
               SCOP domains d1xu1d_ D: A proliferation-inducing ligand, APRIL                                                                                         SCOP domains
               CATH domains 1xu1D00 D:105-241  [code=2.60.120.40, no name defined]                                                                                    CATH domains
           Pfam domains (1) ------------------------TNF-1xu1D01 D:129-241                                                                                             Pfam domains (1)
           Pfam domains (2) ------------------------TNF-1xu1D02 D:129-241                                                                                             Pfam domains (2)
           Pfam domains (3) ------------------------TNF-1xu1D03 D:129-241                                                                                             Pfam domains (3)
         Sec.struct. author ...eeeeeeeeee.......eeeeeeeeeee...eeee..eeee...eeeeeeeeeeee....eeeeeeeee....eeeeeeeeee........eeeeeeeeeeee....eeeeee..............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TNF_2  PDB: D:108-241 UniProt: 108-241                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------TNF_1            ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xu1 D 105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
                                   114       124       134       144       154       164       174       184       194       204       214       224       234

Chain R from PDB  Type:PROTEIN  Length:38
 aligned with TR13B_HUMAN | O14836 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:38
                                    77        87        97        
          TR13B_HUMAN    68 SLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCE 105
               SCOP domains d1xu1r_ R:                             SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeee....eeee.hhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------R- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: R:68-105 [INCOMPLETE]   Transcript 1
                 1xu1 R  68 SLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCE 105
                                    77        87        97

Chain S from PDB  Type:PROTEIN  Length:36
 aligned with TR13B_HUMAN | O14836 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:36
                                    80        90       100      
          TR13B_HUMAN    71 CRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCEN 106
               SCOP domains d1xu1s_ S:                           SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hhhh.eeee....eeeehhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------R-- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.3  PDB: S:71-106 [INCOMPLETE] Transcript 1
                 1xu1 S  71 CRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCEN 106
                                    80        90       100

Chain T from PDB  Type:PROTEIN  Length:39
 aligned with TR13B_HUMAN | O14836 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:39
                                    80        90       100         
          TR13B_HUMAN    71 CRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLR 109
               SCOP domains d1xu1t_ T:                              SCOP domains
               CATH domains --------------------------------------- CATH domains
           Pfam domains (1) TACI-CRD2-1xu1T01 T:71-109              Pfam domains (1)
           Pfam domains (2) TACI-CRD2-1xu1T02 T:71-109              Pfam domains (2)
           Pfam domains (3) TACI-CRD2-1xu1T03 T:71-109              Pfam domains (3)
         Sec.struct. author .hhhh.eeee....eeee.hhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------R----- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: T:71-109 UniProt: 67-149 Transcript 1
                 1xu1 T  71 CRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLR 109
                                    80        90       100

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: TNF-like (100)

Superfamily: TNF-like (100)

Family: TNF-like (82)

Protein domain: A proliferation-inducing ligand, APRIL (5)

Mouse (Mus musculus) [TaxId: 10090] (5)

1a	d1xu1a_	A:
1b	d1xu1b_	B:
1c	d1xu1d_	D:

Class: Small proteins (3458)

Fold: TNF receptor-like (25)

Superfamily: TNF receptor-like (25)

Family: BAFF receptor-like (7)

Protein domain: Tumor necrosis factor receptor superfamily member 13B, TACI (2)

Human (Homo sapiens) [TaxId: 9606] (2)

2a	d1xu1r_	R:
2b	d1xu1s_	S:
2c	d1xu1t_	T:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.40, no name defined] (56)

House mouse (Mus musculus) (14)

1a	1xu1A00	A:105-241
1b	1xu1B00	B:105-241
1c	1xu1D00	D:105-241

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C1q_TNF (45)

Family: TNF (37)

Mus musculus (Mouse) (11)

1a	TNF-1xu1D01	D:129-241
1b	TNF-1xu1D02	D:129-241
1c	TNF-1xu1D03	D:129-241

Clan: no clan defined [family: TACI-CRD2] (2)

Family: TACI-CRD2 (2)

Homo sapiens (Human) (2)

2a	TACI-CRD2-1xu1T01	T:71-109
2b	TACI-CRD2-1xu1T02	T:71-109
2c	TACI-CRD2-1xu1T03	T:71-109

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,D (TNF13_MOUSE | Q9D777)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0005164	tumor necrosis factor receptor binding	Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0016064	immunoglobulin mediated immune response	An immune response mediated by immunoglobulins, whether cell-bound or in solution.
	GO:0002426	immunoglobulin production in mucosal tissue	The synthesis and release of immunoglobulin in the mucosal tissue.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0002636	positive regulation of germinal center formation	Any process that activates or increases the frequency, rate, or extent of germinal center formation.
	GO:0048298	positive regulation of isotype switching to IgA isotypes	Any process that activates or increases the frequency, rate or extent of isotype switching to IgA isotypes.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain R,S,T (TR13B_HUMAN | O14836)

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).
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0001782	B cell homeostasis	The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0002244	hematopoietic progenitor cell differentiation	The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0030889	negative regulation of B cell proliferation	Any process that stops, prevents or reduces the rate or extent of B cell proliferation.
	GO:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005887	integral component of plasma membrane	The component of the plasma 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: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.

Asymmetric/Biological Unit
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	1xu1
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	TNF13_MOUSE \| Q9D777
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	TR13B_HUMAN \| O14836
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	609529
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	TNF13_MOUSE \| Q9D777
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UniProtKB/Swiss-Prot
	TNF13_MOUSE \| Q9D777	:	1u5x 1u5y 1u5z 1xu2 3k48
	TR13B_HUMAN \| O14836	:	1xut

1u5x	APRIL
1u5y	APRIL
1u5z	APRIL
1xu2
1xut

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (12, 12)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

PROSITE Motifs (2, 6)

Exons (1, 3)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 6)

CATH Domains (1, 3)

Pfam Domains (2, 6)

Gene Ontology (27, 30)

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