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(-) Description

Title :  ALU DOMAIN OF THE MAMMALIAN SRP (POTENTIAL ALU RETROPOSITION INTERMEDIATE)
 
Authors :  O. Weichenrieder, K. Wild, K. Strub, S. Cusack
Date :  29 Sep 00  (Deposition) - 08 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alu Ribonucleoprotein Particle, Alu Rnp Assembly And Dimerisation, Translational Control, Alu Retroposition (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Weichenrieder, K. Wild, K. Strub, S. Cusack
Structure And Assembly Of The Alu Domain Of The Mammalian Signal Recognition Particle
Nature V. 408 167 2000
PubMed-ID: 11089964  |  Reference-DOI: 10.1038/35041507

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
    Cellular LocationCYTOPLASM, NUCLEUS?
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    PlasmidPEH9
    SynonymSRP9
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
    Cellular LocationCYTOPLASM, NUCLEUS?
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTRUNCATED AFTER K107
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    PlasmidPEH14DELTAR
    SynonymSRP14
 
Molecule 3 - 7SL RNA, 88-MER
    Cellular LocationCYTOPLASM, NUCLEUS
    ChainsC
    FragmentALU RNA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsG101-U164 AND A383-U399 OF 7SL RNA CIRCULAR PERMUTATION (G101 LINKED TO U399) ADDITIONAL NUCLEOTIDES: 5' G380, C381, U382 AND 3' A165, G166, U167, C168
    Other Details - SourceTHE RNA WAS PRODUCED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE USING RIBOZYME TECHNOLOGY.
    PlasmidPSA88(2)H
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EU32Ligand/IonEUROPIUM (III) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA C:156BINDING SITE FOR RESIDUE EU3 C1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E8S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E8S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028058S68ISRP14_HUMANPolymorphism1802600BS68I

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E8S)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002678841ENSE00001099640chr15:40331389-4033129496SRP14_HUMAN1-881B:2-87
1.2ENST000002678842ENSE00000942420chr15:40331149-4033107773SRP14_HUMAN9-33251B:9-3325
1.3ENST000002678843ENSE00000942421chr15:40330595-40330483113SRP14_HUMAN33-70381B:33-70 (gaps)38
1.4ENST000002678844ENSE00000942422chr15:40329219-4032918733SRP14_HUMAN71-81111B:71-8111
1.5ENST000002678845ENSE00001099638chr15:40328701-40327891811SRP14_HUMAN82-136551B:82-9514

2.1aENST000003047861aENSE00001442734chr1:225965531-225965714184SRP09_HUMAN1-24241A:5-2420
2.2ENST000003047862ENSE00000961765chr1:225971002-22597107069SRP09_HUMAN25-47231A:25-4723
2.5bENST000003047865bENSE00001838300chr1:225976942-2259781681227SRP09_HUMAN48-86391A:48-7528

(-) 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:71
 aligned with SRP09_HUMAN | P49458 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:71
                                    14        24        34        44        54        64        74 
          SRP09_HUMAN     5 QTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVA  75
               SCOP domains d1e8sa_ A: Signal recognition particle 9KDa protein, SRP9               SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1a           Exon 2.2  PDB: A:25-47 Exon 2.5b  PDB: A:48-75      Transcript 2
                 1e8s A   5 QTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVA  75
                                    14        24        34        44        54        64        74 

Chain B from PDB  Type:PROTEIN  Length:76
 aligned with SRP14_HUMAN | P37108 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:94
                                    11        21        31        41        51        61        71        81        91    
          SRP14_HUMAN     2 VLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
               SCOP domains d1e8sb_ B: Signal recognition part                  icle 14KDa protein, SRP14                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................------------------.......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------I--------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1    Exon 1.2  PDB: B:9-33    -------------------------------------Exon 1.4   Exon 1.5       Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3  PDB: B:33-70 (gaps)         ------------------------- Transcript 1 (2)
                 1e8s B   2 VLLESEQFLTELTRLFQKCRTSGSVYITLKKYDG------------------NKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
                                    11        21        31   |     -         -  |     61        71        81        91    
                                                            35                 54                                         

Chain C from PDB  Type:RNA  Length:86
                                                                                                                      
                 1e8s C 380 GCUAGCGAGACCCCGUCUCUGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGGUGGGAGGAUCGCUAG 166
                                   389       399|      110       120       130       140       150       160      
                                             399|                                                                 
                                              101                                                                 

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1E8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E8S)

(-) Gene Ontology  (18, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRP09_HUMAN | P49458)
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.
    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:0005047    signal recognition particle binding    Interacting selectively and non-covalently with the signal recognition particle.
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:0006616    SRP-dependent cotranslational protein targeting to membrane, translocation    The process during cotranslational membrane targeting wherein proteins move across a membrane. SRP and its receptor initiate the transfer of the nascent chain across the endoplasmic reticulum (ER) membrane; they then dissociate from the chain, which is transferred to a set of transmembrane proteins, collectively called the translocon. Once the nascent chain translocon complex is assembled, the elongating chain passes directly from the large ribosomal subunit into the centers of the translocon, a protein-lined channel within the membrane. The growing chain is never exposed to the cytosol and does not fold until it reaches the ER lumen.
    GO:0045900    negative regulation of translational elongation    Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0048500    signal recognition particle    A complex of protein and RNA which facilitates translocation of proteins across membranes.
    GO:0005785    signal recognition particle receptor complex    A transmembrane heterodimeric protein located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex.
    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.

Chain B   (SRP14_HUMAN | P37108)
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.
    GO:0030942    endoplasmic reticulum signal peptide binding    Interacting selectively and non-covalently with an endoplasmic reticulum signal peptide, a specific peptide sequence that acts as a signal to localize the protein within the endoplasmic reticulum.
    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).
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:0045047    protein targeting to ER    The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SRP09_HUMAN | P494581e8o 1ry1 4uyj 4uyk 5aox
        SRP14_HUMAN | P371081e8o 1ry1 4uyj 4uyk 5aox

(-) Related Entries Specified in the PDB File

1e8o CORE OF THE ALU DOMAIN OF THE MAMMALIAN SRP