Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF STALL-1 OF TNF FAMILY LIGAND
 
Authors :  Y. Liu, L. Xu, N. Opalka, H. -B. Shu, G. Zhang
Date :  27 Jun 01  (Deposition) - 08 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J  (1x)
Biol. Unit 2:  A,B,C,D,E,F,G,H,I,J  (6x)
Keywords :  Tall-1, Blys, Thank, Baff, Immune System, Antitumor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, L. Xu, N. Opalka, J. Kappler, H. B. Shu, G. Zhang
Crystal Structure Of Stall-1 Reveals A Virus-Like Assembly Of Tnf Family Ligands.
Cell(Cambridge, Mass. ) V. 108 383 2002
PubMed-ID: 11853672  |  Reference-DOI: 10.1016/S0092-8674(02)00631-1

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: STALL-1, SOLUBLE PART OF TALL-1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TNF FAMILY LIGAND

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): ABCDEFGHIJ
Biological Unit 2 (6x): ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JH5)

(-) Sites  (0, 0)

(no "Site" information available for 1JH5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JH5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JH5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JH5)

(-) PROSITE Motifs  (1, 10)

Asymmetric Unit (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TN13B_HUMAN148-284
 
 
 
 
 
 
 
 
 		  10A:7-143
B:7-143
C:7-143
D:7-143
E:7-143
F:7-143
G:7-143
H:7-143
I:7-143
J:7-143
Biological Unit 1 (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TN13B_HUMAN148-284
 
 
 
 
 
 
 
 
 		  10A:7-143
B:7-143
C:7-143
D:7-143
E:7-143
F:7-143
G:7-143
H:7-143
I:7-143
J:7-143
Biological Unit 2 (1, 60)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TN13B_HUMAN148-284
 
 
 
 
 
 
 
 
 		  60A:7-143
B:7-143
C:7-143
D:7-143
E:7-143
F:7-143
G:7-143
H:7-143
I:7-143
J:7-143

(-) Exons   (5, 50)

Asymmetric Unit (5, 50)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003758872bENSE00001811977chr13:108922066-108922582517TN13B_HUMAN1-1131130--
1.2eENST000003758872eENSE00000686291chr13:108922688-10892277285TN13B_HUMAN114-1422910A:1-1
B:1-1
C:1-1
D:1-1
E:1-1
F:1-1
G:1-1
H:1-1
I:1-1
J:1-1		1
1
1
1
1
1
1
1
1
1
1.3ENST000003758873ENSE00000854068chr13:108939151-10893920757TN13B_HUMAN142-1612010A:1-20
B:1-20
C:1-20
D:1-20
E:1-20
F:1-20
G:1-20
H:1-20
I:1-20
J:1-20		20
20
20
20
20
20
20
20
20
20
1.5aENST000003758875aENSE00000854071chr13:108955601-108955713113TN13B_HUMAN161-1983810A:20-57
B:20-57
C:20-57
D:20-57
E:20-57
F:20-57
G:20-57
H:20-57
I:20-57
J:20-57		38
38
38
38
38
38
38
38
38
38
1.5cENST000003758875cENSE00000854073chr13:108955802-108955952151TN13B_HUMAN199-2495110A:58-108
B:58-108
C:58-108
D:58-108
E:58-108
F:58-108
G:58-108
H:58-108
I:58-108
J:58-108		51
51
51
51
51
51
51
51
51
51
1.6cENST000003758876cENSE00001925016chr13:108959174-108959385212TN13B_HUMAN249-2853710A:108-144
B:108-144
C:108-144
D:108-144
E:108-144
F:108-144
G:108-144
H:108-144
I:108-144
J:108-144		37
37
37
37
37
37
37
37
37
37

(-) 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:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5a_ A: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5A00 A:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: A:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: A:20-57               Exon 1.5c  PDB: A:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: A:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: A:108-144             Transcript 1 (2)
                 1jh5 A   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5b_ B: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5B00 B:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: B:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: B:20-57               Exon 1.5c  PDB: B:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: B:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: B:108-144             Transcript 1 (2)
                 1jh5 B   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain C from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5c_ C: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5C00 C:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: C:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: C:20-57               Exon 1.5c  PDB: C:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: C:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: C:108-144             Transcript 1 (2)
                 1jh5 C   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain D from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5d_ D: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5D00 D:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: D:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: D:20-57               Exon 1.5c  PDB: D:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: D:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: D:108-144             Transcript 1 (2)
                 1jh5 D   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain E from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5e_ E: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5E00 E:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: E:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: E:20-57               Exon 1.5c  PDB: E:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: E:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: E:108-144             Transcript 1 (2)
                 1jh5 E   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain F from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5f_ F: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5F00 F:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: F:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: F:20-57               Exon 1.5c  PDB: F:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: F:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: F:108-144             Transcript 1 (2)
                 1jh5 F   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain G from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5g_ G: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5G00 G:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: G:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: G:20-57               Exon 1.5c  PDB: G:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: G:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: G:108-144             Transcript 1 (2)
                 1jh5 G   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain H from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5h_ H: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5H00 H:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: H:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: H:20-57               Exon 1.5c  PDB: H:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: H:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: H:108-144             Transcript 1 (2)
                 1jh5 H   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain I from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5i_ I: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5I00 I:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: I:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: I:20-57               Exon 1.5c  PDB: I:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: I:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: I:108-144             Transcript 1 (2)
                 1jh5 I   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain J from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d1jh5j_ J: Soluble part of TALL-1, sTALL-1 (BAFF)                                                                                                SCOP domains
               CATH domains 1jh5J00 J:1-144  [code=2.60.120.40, no name defined]                                                                                             CATH domains
           Pfam domains (1) --------------------------TNF-1jh5J01 J:27-143                                                                                                 - Pfam domains (1)
           Pfam domains (2) --------------------------TNF-1jh5J02 J:27-143                                                                                                 - Pfam domains (2)
           Pfam domains (3) --------------------------TNF-1jh5J03 J:27-143                                                                                                 - Pfam domains (3)
           Pfam domains (4) --------------------------TNF-1jh5J04 J:27-143                                                                                                 - Pfam domains (4)
           Pfam domains (5) --------------------------TNF-1jh5J05 J:27-143                                                                                                 - Pfam domains (5)
           Pfam domains (6) --------------------------TNF-1jh5J06 J:27-143                                                                                                 - Pfam domains (6)
           Pfam domains (7) --------------------------TNF-1jh5J07 J:27-143                                                                                                 - Pfam domains (7)
           Pfam domains (8) --------------------------TNF-1jh5J08 J:27-143                                                                                                 - Pfam domains (8)
           Pfam domains (9) --------------------------TNF-1jh5J09 J:27-143                                                                                                 - Pfam domains (9)
          Pfam domains (10) --------------------------TNF-1jh5J10 J:27-143                                                                                                 - Pfam domains (10)
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....eeeeeeeee..........eeeeeeeeee.........eeeeeeeee....eeeee.......ee......ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: J:7-143 UniProt: 148-284                                                                                                     - PROSITE
           Transcript 1 (1) 1------------------Exon 1.5a  PDB: J:20-57               Exon 1.5c  PDB: J:58-108 UniProt: 199-249          ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: J:1-2---------------------------------------------------------------------------------------Exon 1.6c  PDB: J:108-144             Transcript 1 (2)
                 1jh5 J   1 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 10)

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

(-) CATH Domains  (1, 10)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: [code=2.60.120.40, no name defined] (56)
(-)
Human (Homo sapiens) (38)
1a1jh5A00A:1-144
1b1jh5B00B:1-144
1c1jh5C00C:1-144
1d1jh5D00D:1-144
1e1jh5E00E:1-144
1f1jh5F00F:1-144
1g1jh5G00G:1-144
1h1jh5H00H:1-144
1i1jh5I00I:1-144
1j1jh5J00J:1-144

(-) Pfam Domains  (1, 10)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)
(-)
Family: TNF (37)
(-)
Homo sapiens (Human) (26)
1aTNF-1jh5J01J:27-143
1bTNF-1jh5J02J:27-143
1cTNF-1jh5J03J:27-143
1dTNF-1jh5J04J:27-143
1eTNF-1jh5J05J:27-143
1fTNF-1jh5J06J:27-143
1gTNF-1jh5J07J:27-143
1hTNF-1jh5J08J:27-143
1iTNF-1jh5J09J:27-143
1jTNF-1jh5J10J:27-143

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (TN13B_HUMAN | Q9Y275)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1jh5)
 
  Sites
(no "Sites" information available for 1jh5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jh5)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1jh5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TN13B_HUMAN | Q9Y275
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TN13B_HUMAN | Q9Y275
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TN13B_HUMAN | Q9Y275: 1kd7 1kxg 1oqd 1oqe 1osg 3v56 4v46 4zch

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JH5)