1XU2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURE OF APRIL BOUND TO BCMA

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 :   2.35

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	:	PET32A (MODIFIED)
	Expression System Strain	:	ORIGAMI(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TNF DOMAIN OF APRIL
	Gene	:	TNFSF13, APRIL
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	A PROLIFERATION-INDUCING LIGAND, APRIL, TNFSF13B OR TALL-2

Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 17
	Chains	:	R, S, T
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PZCT
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BCMA ECD
	Gene	:	TNFRSF17, BCM, BCMA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	B-CELL MATURATION PROTEIN, TNFFSF17

		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 , HIS B:106 , HIS D:106	BINDING SITE FOR RESIDUE NI B 301

Asymmetric/Biological Unit

No.	Residues
1	A:187	-	A:202
2	B:187	-	B:202
3	D:187	-	D:202
4	R:8	-	R:21
5	R:24	-	R:37
6	R:28	-	R:41
7	S:8	-	S:21
8	S:24	-	S:37
9	S:28	-	S:41
10	T:8	-	T:21
11	T:24	-	T:37
12	T:28	-	T:41

(no "Cis Peptide Bond" information available for 1XU2)

(no "SAP(SNP)/Variant" information available for 1XU2)

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	ENST00000053243	1	ENSE00000829755	chr16:12058964-12059311	348	TNR17_HUMAN	1-44	44	3	R:8-43 S:6-42 T:8-42	36 37 35
1.2	ENST00000053243	2	ENSE00000668477	chr16:12060052-12060198	147	TNR17_HUMAN	44-93	50	0	-	-
1.4	ENST00000053243	4	ENSE00001722330	chr16:12061427-12061925	499	TNR17_HUMAN	93-184	92	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 d1xu2a_ A: A proliferation-inducing ligand, APRIL                                                                                         SCOP domains
               CATH domains 1xu2A00 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....eeeeeeeee....eeeeeeeeee...hhhh.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
                 1xu2 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 d1xu2b_ B: A proliferation-inducing ligand, APRIL                                                                                         SCOP domains
               CATH domains 1xu2B00 B:105-241  [code=2.60.120.40, no name defined]                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.......eeeeeeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee....eeeeeeeeee.........eeeeeeeeeee....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
                 1xu2 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 d1xu2d_ D: A proliferation-inducing ligand, APRIL                                                                                         SCOP domains
               CATH domains 1xu2D00 D:105-241  [code=2.60.120.40, no name defined]                                                                                    CATH domains
           Pfam domains (1) ------------------------TNF-1xu2D01 D:129-241                                                                                             Pfam domains (1)
           Pfam domains (2) ------------------------TNF-1xu2D02 D:129-241                                                                                             Pfam domains (2)
           Pfam domains (3) ------------------------TNF-1xu2D03 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
                 1xu2 D 105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
                                   114       124       134       144       154       164       174       184       194       204       214       224       234

Chain R from PDB  Type:PROTEIN  Length:36
 aligned with TNR17_HUMAN | Q02223 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:36
                                    17        27        37      
          TNR17_HUMAN     8 CSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCNA  43
               SCOP domains d1xu2r_ R:                           SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ....eeee....eeee.hhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: R:8-43 UniProt: 1-44  Transcript 1
                 1xu2 R   8 CSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCNA  43
                                    17        27        37

Chain S from PDB  Type:PROTEIN  Length:37
 aligned with TNR17_HUMAN | Q02223 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:37
                                    15        25        35       
          TNR17_HUMAN     6 GQCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCN  42
               SCOP domains d1xu2s_ S:                            SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ......eeee....eeee.hhhh........hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: S:6-42 UniProt: 1-44   Transcript 1
                 1xu2 S   6 GQCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCN  42
                                    15        25        35

Chain T from PDB  Type:PROTEIN  Length:35
 aligned with TNR17_HUMAN | Q02223 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:35
                                    17        27        37     
          TNR17_HUMAN     8 CSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCN  42
               SCOP domains d1xu2t_ T:                          SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) BCMA-Tall_bind-1xu2T01 T:8-42       Pfam domains (1)
           Pfam domains (2) BCMA-Tall_bind-1xu2T02 T:8-42       Pfam domains (2)
           Pfam domains (3) BCMA-Tall_bind-1xu2T03 T:8-42       Pfam domains (3)
         Sec.struct. author ....eeee....eeee.hhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: T:8-42 UniProt: 1-44 Transcript 1
                 1xu2 T   8 CSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCN  42
                                    17        27        37

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	d1xu2a_	A:
1b	d1xu2b_	B:
1c	d1xu2d_	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 17, BCMA (2)

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

2a	d1xu2r_	R:
2b	d1xu2s_	S:
2c	d1xu2t_	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	1xu2A00	A:105-241
1b	1xu2B00	B:105-241
1c	1xu2D00	D:105-241

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C1q_TNF (45)

Family: TNF (37)

Mus musculus (Mouse) (11)

1a	TNF-1xu2D01	D:129-241
1b	TNF-1xu2D02	D:129-241
1c	TNF-1xu2D03	D:129-241

Clan: no clan defined [family: BCMA-Tall_bind] (3)

Family: BCMA-Tall_bind (3)

Homo sapiens (Human) (3)

2a	BCMA-Tall_bind-1xu2T01	T:8-42
2b	BCMA-Tall_bind-1xu2T02	T:8-42
2c	BCMA-Tall_bind-1xu2T03	T:8-42

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 (TNR17_HUMAN | Q02223)

molecular function
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	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:0002260	lymphocyte homeostasis	The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	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:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	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: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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	1xu2
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	TNF13_MOUSE \| Q9D777
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	TNR17_HUMAN \| Q02223
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	TNF13_MOUSE \| Q9D777
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UniProtKB/Swiss-Prot
	TNF13_MOUSE \| Q9D777	:	1u5x 1u5y 1u5z 1xu1 3k48
	TNR17_HUMAN \| Q02223	:	1oqd 2kn1 4zfo

1u5x	APRIL
1u5y	APRIL
1u5z	APRIL
1xu1	CRYSTAL STRUCTURE OF APRIL BOUND TO TACI
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 (0, 0)

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 (26, 28)

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