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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TRANSLIN
 
Authors :  I. Sugiura, C. Sasaki, T. Hasegawa, T. Kohno, S. Sugio, H. Moriyama, M. K T. Matsuzaki
Date :  06 Dec 02  (Deposition) - 06 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  D  (2x)
Biol. Unit 3:  A (1x),C (1x)
Biol. Unit 4:  B  (2x)
Biol. Unit 5:  A,B,C,D  (2x)
Keywords :  Testis/Brain Rna Binding Protein, Ssdna Binding Protein, Rna Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Sugiura, C. Sasaki, T. Hasegawa, T. Kohno, S. Sugio, H. Moriyama, M. Kasai, T. Matsuzaki
Structure Of Human Translin At 2. 2 A Resolution.
Acta Crystallogr. , Sect. D V. 60 674 2004
PubMed-ID: 15039555  |  Reference-DOI: 10.1107/S0907444904002549

(-) Compounds

Molecule 1 - TRANSLIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE9
    Expression System Strain: M15[PREP4]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (2x):    D
Biological Unit 3 (1x): A (1x) C (1x) 
Biological Unit 4 (2x):  B  
Biological Unit 5 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1J1J)

(-) Sites  (0, 0)

(no "Site" information available for 1J1J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J1J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile B:54 -Pro B:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J1J)

(-) Exons   (6, 24)

Asymmetric Unit (6, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003896822aENSE00001506653chr2:122513109-122513421313TSN_HUMAN1-22224A:1-22
B:1-22
C:1-22
D:1-22		22
22
22
22
1.4bENST000003896824bENSE00001506652chr2:122514816-12251490994TSN_HUMAN23-54324A:23-54
B:23-54
C:23-54
D:23-54		32
32
32
32
1.5ENST000003896825ENSE00001506651chr2:122516286-12251638297TSN_HUMAN54-86334A:54-86
B:54-86
C:54-86
D:54-86		33
33
33
33
1.6ENST000003896826ENSE00001506650chr2:122518985-122519100116TSN_HUMAN86-125404A:86-125
B:86-125
C:86-125
D:86-125		40
40
40
40
1.7bENST000003896827bENSE00001506649chr2:122520581-12252066080TSN_HUMAN125-151274A:125-151
B:125-151
C:125-151
D:125-151		27
27
27
27
1.8hENST000003896828hENSE00001506648chr2:122522710-1225254292720TSN_HUMAN152-228774A:152-217
B:152-217
C:152-217
D:152-217		66
66
66
66

(-) 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:217
 aligned with TSN_HUMAN | Q15631 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            TSN_HUMAN     1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
               SCOP domains d1j1ja_ A: Translin                                                                                                                                                                                                       SCOP domains
               CATH domains 1j1jA01 A:1-132 Translin; domain 1                                                                                                  1j1jA02 A:133-217 Translin; domain 2                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-22Exon 1.4b  PDB: A:23-54         -------------------------------Exon 1.6  PDB: A:86-125 UniProt: 86-125 --------------------------Exon 1.8h  PDB: A:152-217 UniProt: 152-228 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.5  PDB: A:54-86           --------------------------------------Exon 1.7b  PDB: A:125-151  ------------------------------------------------------------------ Transcript 1 (2)
                 1j1j A   1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with TSN_HUMAN | Q15631 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            TSN_HUMAN     1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
               SCOP domains d1j1jb_ B: Translin                                                                                                                                                                                                       SCOP domains
               CATH domains 1j1jB01 B:1-132 Translin; domain 1                                                                                                  1j1jB02 B:133-217 Translin; domain 2                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-22Exon 1.4b  PDB: B:23-54         -------------------------------Exon 1.6  PDB: B:86-125 UniProt: 86-125 --------------------------Exon 1.8h  PDB: B:152-217 UniProt: 152-228 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.5  PDB: B:54-86           --------------------------------------Exon 1.7b  PDB: B:125-151  ------------------------------------------------------------------ Transcript 1 (2)
                 1j1j B   1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with TSN_HUMAN | Q15631 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            TSN_HUMAN     1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
               SCOP domains d1j1jc_ C: Translin                                                                                                                                                                                                       SCOP domains
               CATH domains 1j1jC01 C:1-132 Translin; domain 1                                                                                                  1j1jC02 C:133-217 Translin; domain 2                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: C:1-22Exon 1.4b  PDB: C:23-54         -------------------------------Exon 1.6  PDB: C:86-125 UniProt: 86-125 --------------------------Exon 1.8h  PDB: C:152-217 UniProt: 152-228 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.5  PDB: C:54-86           --------------------------------------Exon 1.7b  PDB: C:125-151  ------------------------------------------------------------------ Transcript 1 (2)
                 1j1j C   1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain D from PDB  Type:PROTEIN  Length:217
 aligned with TSN_HUMAN | Q15631 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            TSN_HUMAN     1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
               SCOP domains d1j1jd_ D: Translin                                                                                                                                                                                                       SCOP domains
               CATH domains 1j1jD01 D:1-132 Translin; domain 1                                                                                                  1j1jD02 D:133-217 Translin; domain 2                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: D:1-22Exon 1.4b  PDB: D:23-54         -------------------------------Exon 1.6  PDB: D:86-125 UniProt: 86-125 --------------------------Exon 1.8h  PDB: D:152-217 UniProt: 152-228 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.5  PDB: D:54-86           --------------------------------------Exon 1.7b  PDB: D:125-151  ------------------------------------------------------------------ Transcript 1 (2)
                 1j1j D   1 MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGF 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J1J)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TSN_HUMAN | Q15631)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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    Ile B:54 - Pro B:55   [ RasMol ]  
 
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  1j1j
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  TSN_HUMAN | Q15631
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 Related Entries

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

UniProtKB/Swiss-Prot
        TSN_HUMAN | Q15631: 3pja 3qb5 4wyv

(-) Related Entries Specified in the PDB File

1key