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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN-RNA COMPLEX
 
Authors :  J. Ding, D. C. Wang
Date :  20 May 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,X,Y
Keywords :  Protein-Rna Complex, Dna/Rna Binding, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Guo, J. Ding, R. Guo, Y. Hou, D. C. Wang, L. Huang
Biochemical And Structural Insights Into Rna Binding By Ssh10B, A Member Of The Highly Conserved Sac10B Family In Archaea
J. Biol. Chem. 2013
PubMed: search  |  Reference-DOI: 10.1074/JBC.M113.521351

(-) Compounds

Molecule 1 - DNA/RNA-BINDING PROTEIN ALBA 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALBA1, SSH10B
    Organism Scientific: SULFOLOBUS SHIBATAE
    Organism Taxid: 2286
    Strain: 2286
    Synonym: SSH10B
 
Molecule 2 - RNA (25-MER)
    Chains: X, Y
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDXY

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3WBM)

(-) Sites  (0, 0)

(no "Site" information available for 3WBM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WBM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WBM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WBM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WBM)

(-) Exons   (0, 0)

(no "Exon" information available for 3WBM)

(-) Sequences/Alignments

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:86
 aligned with ALBA1_SULSH | P60848 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:93
                                    14        24        34        44        54        64        74        84        94   
           ALBA1_SULSH    5 TPTPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDGRQSRVSTIEIAIRKK 97
               SCOP domains d3wbma_ A: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeeeee..-------..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3wbm A  5 TPTPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVV-------SRVSTIEIAIRKK 97
                                    14        24        34        44        54        64        74  |      -|       94   
                                                                                                   77      85            


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with ALBA1_SULSH | P60848 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:91
                                    16        26        36        46        56        66        76        86        96 
           ALBA1_SULSH    7 TPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDGRQSRVSTIEIAIRKK 97
               SCOP domains d3wbmb_ B: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh.....eeeeeeeeeee..-------..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3wbm B  7 TPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVV-------SRVSTIEIAIRKK 97
                                    16        26        36        46        56        66        76|       86        96 
                                                                                                 77      85            


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with ALBA1_SULSH | P60848 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:93
                                    14        24        34        44        54        64        74        84        94   
           ALBA1_SULSH    5 TPTPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDGRQSRVSTIEIAIRKK 97
               SCOP domains d3wbmc_ C: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh.....eeeeeeeeeee..-------..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3wbm C  5 TPTPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVV-------SRVSTIEIAIRKK 97
                                    14        24        34        44        54        64        74  |      -|       94   
                                                                                                   77      85            


Chain D from PDB  Type:PROTEIN  Length:89
 aligned with ALBA1_SULSH | P60848 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:89
                                    18        28        38        48        58        68        78        88         
           ALBA1_SULSH    9 SNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDGRQSRVSTIEIAIRKK 97
               SCOP domains d3wbmd_ D: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh....eeeeeeeeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3wbm D  9 SNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDGRQSRVSTIEIAIRKK 97
                                    18        28        38        48        58        68        78        88         


Chain X from PDB  Type:RNA  Length:25
                                                        
                  3wbm X  1 GGUAAGAGCACCCGACUGCUCUUCC 25
                                    10        20     


Chain Y from PDB  Type:RNA  Length:25
                                                        
                  3wbm Y  1 GGUAAGAGCACCCGACUGCUCUUCC 25
                                    10        20
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WBM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WBM)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ALBA1_SULSH | P60848)
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:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3wbm
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALBA1_SULSH | P60848: 1h0x 1h0y 1y9x

(-) Related Entries Specified in the PDB File

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