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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF A TERNARY S-DOMAIN COMPLEX OF HUMAN SIGNAL RECOGNITION PARTICLE
 
Authors :  A. Kuglstatter, C. Oubridge, K. Nagai
Date :  13 Aug 02  (Deposition) - 20 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rna-Protein Complex, A-Minor Motif, 3-Helix Junction, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuglstatter, C. Oubridge, K. Nagai
Induced Structural Changes Of 7Sl Rna During The Assembly Of Human Signal Recognition Particle
Nat. Struct. Biol. V. 9 740 2002
PubMed-ID: 12244299  |  Reference-DOI: 10.1038/NSB843
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 7S RNA OF HUMAN SRP
    Chains: A
    Engineered: YES
    Expression System Plasmid: PUC18
    Expression System Vector Type: PLASMID
    Fragment: S-DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE 19KDA PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23D
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SRP19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP19
 
Molecule 3 - SIGNAL RECOGNITION PARTICLE 54KDA PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRK172
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: M-DOMAIN
    Gene: SRP54
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP54

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3MG5Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA A:192 , G A:193 , G A:194BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREA A:183 , C A:185BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREA A:205BINDING SITE FOR RESIDUE MG A 503
4AC4SOFTWAREA A:183BINDING SITE FOR RESIDUE MG A 504
5AC5SOFTWAREC A:116 , U A:117BINDING SITE FOR RESIDUE MG A 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002167741ENSE00001359255chr14:35452231-35452421191SRP54_HUMAN-00--
1.2ENST000002167742ENSE00000889679chr14:35465883-35465993111SRP54_HUMAN1-26260--
1.3ENST000002167743ENSE00000655760chr14:35468764-3546885592SRP54_HUMAN27-57310--
1.4ENST000002167744ENSE00000655761chr14:35470142-3547022685SRP54_HUMAN57-85290--
1.5ENST000002167745ENSE00000655764chr14:35476489-35476593105SRP54_HUMAN86-120350--
1.6ENST000002167746ENSE00000655766chr14:35477833-3547789967SRP54_HUMAN121-143230--
1.7ENST000002167747ENSE00000655768chr14:35477980-3547803758SRP54_HUMAN143-162200--
1.8ENST000002167748ENSE00000655770chr14:35480715-35480865151SRP54_HUMAN162-212510--
1.9ENST000002167749ENSE00000655772chr14:35482552-35482700149SRP54_HUMAN213-262500--
1.10ENST0000021677410ENSE00000655775chr14:35483008-35483108101SRP54_HUMAN262-296350--
1.11ENST0000021677411ENSE00000655777chr14:35483950-3548403687SRP54_HUMAN296-325301C:323-3253
1.12ENST0000021677412ENSE00000655779chr14:35487898-3548797174SRP54_HUMAN325-349251C:325-34925
1.13ENST0000021677413ENSE00000655781chr14:35488172-35488280109SRP54_HUMAN350-386371C:350-386 (gaps)37
1.14ENST0000021677414ENSE00000655783chr14:35492116-35492286171SRP54_HUMAN386-443581C:386-43853
1.15ENST0000021677415ENSE00000655785chr14:35497294-3549738996SRP54_HUMAN443-475330--
1.16ENST0000021677416ENSE00000889680chr14:35498267-35498773507SRP54_HUMAN475-504300--

(-) 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:RNA  Length:128
                                                                                                                                                                
                 1mfq A 112 GACACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGUc 239
                                   121       131       141       151       161       171       181       191       201       211       221       231       |
                                                                                                                                                         239-CCC


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with SRP19_HUMAN | P09132 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:107
                                    23        33        43        53        63        73        83        93       103       113       
          SRP19_HUMAN    14 RFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ 120
               SCOP domains d1mfqb_ B: SRP19                                                                                            SCOP domains
               CATH domains 1mfqB00 B:14-120 SRP19                                                                                      CATH domains
               Pfam domains --SRP19-1mfqB01 B:16-116                                                                               ---- Pfam domains
         Sec.struct. author ..eeehhhhhh....................hhhhhhhhhhhhh.eeeee.................eeeee...............hhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1mfq B  14 RFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ 120
                                    23        33        43        53        63        73        83        93       103       113       


Chain C from PDB  Type:PROTEIN  Length:108
 aligned with SRP54_HUMAN | P61011 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:116
                                   332       342       352       362       372       382       392       402       412       422       432      
          SRP54_HUMAN   323 KHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKMGGIK 438
               SCOP domains d1mfqc_ C: SRP54M                                                                                                    SCOP domains
               CATH domains 1mfqC00 C:323-438  [code=1.10.260        .30, no name defined]                                                       CATH domains
               Pfam domains ---SRP_SPB-1mfqC01 C:326-431                                                                                 ------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..hhhhhhh.......--------.hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1------------------------Exon 1.13  PDB: C:350-386 (gaps)     ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.12  PDB: C:325-349------------------------------------Exon 1.14  PDB: C:386-438 UniProt: 386-443            Transcript 1 (2)
                 1mfq C 323 KHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGF--------NEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKMGGIK 438
                                   332       342       352  |      - |     372       382       392       402       412       422       432      
                                                          355      364
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SRP19] (9)
(-)
Clan: no clan defined [family: SRP_SPB] (20)

(-) Gene Ontology  (25, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (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.

Chain C   (SRP54_HUMAN | P61011)
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:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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: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:0043021    ribonucleoprotein complex binding    Interacting selectively and non-covalently with any complex of RNA and protein.
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:0006617    SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition    The process in which SRP binds to the signal peptide in a nascent protein, causing protein elongation to pause, during cotranslational membrane targeting.
    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: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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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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  SRP54_HUMAN | P61011
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 Related Entries

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

UniProtKB/Swiss-Prot
        SRP19_HUMAN | P09132: 1jid 1ry1 2j37 3ktv 4p3e 5m73
        SRP54_HUMAN | P61011: 1qb2 5l3q

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MFQ)