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(-) Description

Title :  STRUCTURAL BASIS FOR RECOGNITION OF UUUOH 3'-TERMINII OF NASCENT RNA POL III TRANSCRIPTS BY LA AUTOANTIGEN
 
Authors :  M. Teplova, Y. R. Yuan, S. Ilin, L. Malinina, A. T. Phan, A. Teplov, D. J. P
Date :  11 Feb 05  (Deposition) - 17 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Rna Complex, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Teplova, Y. R. Yuan, A. T. Phan, L. Malinina, S. Ilin, A. Teplov, D. J. Patel
Structural Basis For Recognition And Sequestration Of Uuu(Oh) 3' Temini Of Nascent Rna Polymerase Iii Transcripts By La, A Rheumatic Disease Autoantigen.
Mol. Cell V. 21 75 2006
PubMed-ID: 16387655  |  Reference-DOI: 10.1016/J.MOLCEL.2005.10.027

(-) Compounds

Molecule 1 - 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
    ChainsC, D
    EngineeredYES
    SyntheticYES
 
Molecule 2 - LUPUS LA PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET28B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-194
    GeneSSB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSJOGREN SYNDROME TYPE B ANTIGEN, SS-B, LA RIBONUCLEOPROTEIN, LA AUTOANTIGEN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1YTY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034066P48SLA_HUMANPolymorphism17160793A/BP48S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034066P48SLA_HUMANPolymorphism17160793AP48S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034066P48SLA_HUMANPolymorphism17160793BP48S

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LAPS50961 La-type HTH domain profile.LA_HUMAN7-99
 
  2A:7-99
B:7-99
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.LA_HUMAN111-187
 
  2A:111-187
B:111-187
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LAPS50961 La-type HTH domain profile.LA_HUMAN7-99
 
  1A:7-99
-
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.LA_HUMAN111-187
 
  1A:111-187
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LAPS50961 La-type HTH domain profile.LA_HUMAN7-99
 
  1-
B:7-99
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.LA_HUMAN111-187
 
  1-
B:111-187

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002609562aENSE00001893329chr2:170655322-170655486165LA_HUMAN-00--
1.4ENST000002609564ENSE00002156069chr2:170657462-17065753675LA_HUMAN1-22222A:6-22
B:7-22
17
16
1.5ENST000002609565ENSE00001610086chr2:170661984-170662087104LA_HUMAN23-57352A:23-57
B:23-57
35
35
1.6aENST000002609566aENSE00000782038chr2:170662175-170662349175LA_HUMAN57-115592A:57-115
B:57-115
59
59
1.7cENST000002609567cENSE00000782039chr2:170663295-170663402108LA_HUMAN116-151362A:116-151
B:116-151
36
36
1.7gENST000002609567gENSE00002168098chr2:170663481-170663581101LA_HUMAN152-185342A:152-185
B:152-185
34
34
1.8cENST000002609568cENSE00000782041chr2:170664992-17066506372LA_HUMAN185-209252A:185-189
B:185-189
5
5
1.8eENST000002609568eENSE00000782042chr2:170665370-17066541243LA_HUMAN209-223150--
1.9cENST000002609569cENSE00000782043chr2:170666793-170666933141LA_HUMAN224-270470--
1.10bENST0000026095610bENSE00000782044chr2:170667368-170667554187LA_HUMAN271-333630--
1.11ENST0000026095611ENSE00000782045chr2:170667693-170667833141LA_HUMAN333-380480--
1.12bENST0000026095612bENSE00001588653chr2:170668178-170668574397LA_HUMAN380-408290--

(-) 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:184
 aligned with LA_HUMAN | P05455 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:184
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
             LA_HUMAN     6 DNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYF 189
               SCOP domains d1ytya1 A:6-103 Lupus La autoantigen N-terminal domain                                            d1ytya2 A:104-189 Lupus LA protein                                                     SCOP domains
               CATH domains 1ytyA01 A:6-90 'winged helix' repressor DNA binding domain                           ---------1ytyA02 A:100-189  [code=3.30.70.330, no name defined]                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eehhhhh.hhhhhhhh.hhhhhhhhhhh.....eee.....eeee.........hhhhhhhhhhheeeee......hhhhhhhhhhhhh.eeeeeeee.....eeeeeeeee.hhhhhhhhhhh...ee..ee.eeee.hhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------S--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LA  PDB: A:7-99 UniProt: 7-99                                                            -----------RRM  PDB: A:111-187 UniProt: 111-187                                         -- PROSITE
           Transcript 1 (1) Exon 1.4         Exon 1.5  PDB: A:23-57             ----------------------------------------------------------Exon 1.7c  PDB: A:116-151           Exon 1.7g  PDB: A:152-185         ---- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.6a  PDB: A:57-115 UniProt: 57-115                   ---------------------------------------------------------------------1.8c  Transcript 1 (2)
                 1yty A   6 DNEKmAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEImIKFNRLNRLTTDFNVIVEALSKSKAELmEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQmRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYF 189
                                |   15        25        35        45      | 55        65        75    |   85        95       105       115       125       135      |145       155       165       175       185    
                                |                                        52-MSE                      80-MSE                                                       142-MSE                                           
                               10-MSE                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with LA_HUMAN | P05455 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:183
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   
             LA_HUMAN     7 NEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYF 189
               SCOP domains d1ytyb1 B:7-103 Lupus La autoantigen N-terminal domain                                           d1ytyb2 B:104-189 Lupus LA protein                                                     SCOP domains
               CATH domains 1ytyB01 B:7-90 'winged helix' repressor DNA binding domain                          ---------1ytyB02 B:100-189  [code=3.30.70.330, no name defined]                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eehhhhh.hhhhhhhh.hhhhhhhhhhh.....eee.....eeee.........hhhhhhhhhh.eeeee......hhhhhhhhhhhh..eeeeeeee.....eeeeeeeee.hhhhhhhhhhh...ee..ee.eeee.hhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------S--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_LA  PDB: B:7-99 UniProt: 7-99                                                            -----------RRM  PDB: B:111-187 UniProt: 111-187                                         -- PROSITE
           Transcript 1 (1) Exon 1.4        Exon 1.5  PDB: B:23-57             ----------------------------------------------------------Exon 1.7c  PDB: B:116-151           Exon 1.7g  PDB: B:152-185         ---- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.6a  PDB: B:57-115 UniProt: 57-115                   ---------------------------------------------------------------------1.8c  Transcript 1 (2)
                 1yty B   7 NEKmAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEImIKFNRLNRLTTDFNVIVEALSKSKAELmEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQmRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYF 189
                               |    16        26        36        46     |  56        66        76   |    86        96       106       116       126       136     | 146       156       166       176       186   
                              10-MSE                                    52-MSE                      80-MSE                                                       142-MSE                                           

Chain C from PDB  Type:RNA  Length:9
                                         
                 1yty C   1 UGCUGUUUU   9

Chain D from PDB  Type:RNA  Length:9
                                         
                 1yty D   1 UGCUGUUUU   9

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LA_HUMAN | P05455)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0075522    IRES-dependent viral translational initiation    Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0008334    histone mRNA metabolic process    The chemical reactions and pathways involving an mRNA encoding a histone.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        LA_HUMAN | P054551owx 1s79 1s7a 1zh5 2vod 2von 2voo 2vop

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