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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN SRP19/S-DOMAIN SRP RNA COMPLEX
 
Authors :  K. Wild, G. Bange, G. Bozkurt, I. Sinning
Date :  26 Nov 09  (Deposition) - 16 Feb 10  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribonucleoprotein Complex, Rna-Rna Tertiary Interactions, Asymmetric Loop, Rna-Binding, Signal Recognition Particle, Rna-Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Wild, G. Bange, G. Bozkurt, B. Segnitz, A. Hendricks, I. Sinning
Structural Insights Into The Assembly Of The Human And Archaeal Signal Recognition Particles.
Acta Crystallogr. , Sect. D V. 66 295 2010
PubMed-ID: 20179341  |  Reference-DOI: 10.1107/S0907444910000879

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21D
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSRP19
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSRP19
 
Molecule 2 - SRP RNA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC19
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentS DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - SRP RNA
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC19
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentS DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GDP1Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
2K3Ligand/IonPOTASSIUM ION
3MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GDP-1Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN D:59 , GLN D:88 , CYS D:94BINDING SITE FOR RESIDUE K D 129
2AC2SOFTWAREG C:193 , G C:194BINDING SITE FOR RESIDUE MG C 4
3AC3SOFTWAREA C:139BINDING SITE FOR RESIDUE MG C 5
4AC4SOFTWAREG A:155 , G A:156BINDING SITE FOR RESIDUE MG A 6

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KTV)

(-) 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:RNA  Length:108
                                                                                                                                            
                 3ktv A 122 GCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGUA 229
                                   131       141       151       161       171       181       191       201       211       221        

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with SRP19_HUMAN | P09132 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:106
                                    19        29        39        49        59        69        79        89        99       109      
          SRP19_HUMAN    10 ADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKL 115
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ktvB00 B:10-115 SRP19                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeehhhhhh....................hhhhhhhhhhh...eeee............hhhhh..eeee.ee...ee......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3ktv B  10 ADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKL 115
                                    19        29        39        49        59        69        79        89        99       109      

Chain C from PDB  Type:RNA  Length:108
                                                                                                                                            
                 3ktv C 122 gCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGUA 229
                            |      131       141       151       161       171       181       191       201       211       221        
                          122-GDP                                                                                                       

Chain D from PDB  Type:PROTEIN  Length:108
 aligned with SRP19_HUMAN | P09132 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:108
                                    17        27        37        47        57        67        77        87        97       107        
          SRP19_HUMAN     8 SPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKL 115
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3ktvD00 D:8-115 SRP19                                                                                        CATH domains
           Pfam domains (1) --------SRP19-3ktvD01 D:16-115                                                                               Pfam domains (1)
           Pfam domains (2) --------SRP19-3ktvD02 D:16-115                                                                               Pfam domains (2)
         Sec.struct. author ........eeehhhhhh...........hhhhh....hhhhhhhhhhh...eeee............hhhhh..eeee.ee...ee......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3ktv D   8 SPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKL 115
                                    17        27        37        47        57        67        77        87        97       107        

   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  (0, 0)

(no "SCOP Domain" information available for 3KTV)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain B,D   (SRP19_HUMAN | P09132)
molecular function
    GO:0008312    7S RNA binding    Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006614    SRP-dependent cotranslational protein targeting to membrane    The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
    GO:0006613    cotranslational protein targeting to membrane    The targeting of proteins to a membrane that occurs during translation. The transport of most secretory proteins, particularly those with more than 100 amino acids, into the endoplasmic reticulum lumen occurs in this manner, as does the import of some proteins into mitochondria.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0048500    signal recognition particle    A complex of protein and RNA which facilitates translocation of proteins across membranes.
    GO:0005786    signal recognition particle, endoplasmic reticulum targeting    A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. Examples of this component are found in Mus musculus, Saccharomyces cerevisiae and Arabidopsis thaliana.

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        SRP19_HUMAN | P091321jid 1mfq 1ry1 2j37 4p3e 5m73

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3ktw