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(-) Description

Title :  STRUCTURES OF SRP54 AND SRP19, THE TWO PROTEINS ASSEMBLING THE RIBONUCLEIC CORE OF THE SIGNAL RECOGNITION PARTICLE FROM THE ARCHAEON PYROCOCCUS FURIOSUS.
 
Authors :  P. F. Egea, J. Napetschnig, P. Walter, R. M. Stroud
Date :  29 Jun 08  (Deposition) - 04 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Rna, Signal Recognition Particle, Cytoplasm, Ribonucleoprotein, Rna-Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Egea, J. Napetschnig, P. Walter, R. M. Stroud
Structures Of Srp54 And Srp19, The Two Proteins That Organize The Ribonucleic Core Of The Signal Recognition Particle From Pyrococcus Furiosus.
Plos One V. 3 E3528 2008
PubMed-ID: 18953414  |  Reference-DOI: 10.1371/JOURNAL.PONE.0003528
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) ROSETTA2
    Expression System Vector Type: PLASMID
    Gene: SRP19, PF1894
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Strain: DSM3638
    Synonym: SRP19

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 40)

Asymmetric/Biological Unit (2, 40)
No.NameCountTypeFull Name
1BR39Ligand/IonBROMIDE ION
2MLI1Ligand/IonMALONATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY C:80 , LYS C:83BINDING SITE FOR RESIDUE BR C 107
02AC2SOFTWARETRP A:7BINDING SITE FOR RESIDUE BR A 107
03AC3SOFTWARETRP D:7BINDING SITE FOR RESIDUE BR D 107
04AC4SOFTWARETRP C:7BINDING SITE FOR RESIDUE BR C 108
05AC5SOFTWAREGLU A:30BINDING SITE FOR RESIDUE BR A 108
06AC6SOFTWAREARG C:3 , PHE C:4 , GLY D:20BINDING SITE FOR RESIDUE BR C 109
07AC7SOFTWAREPHE C:4 , GLU D:10BINDING SITE FOR RESIDUE BR C 112
08AC8SOFTWAREARG A:25 , SER A:26 , ALA A:28 , ARG A:93BINDING SITE FOR RESIDUE BR A 110
09AC9SOFTWARETRP A:7 , GLU A:10 , PHE B:4BINDING SITE FOR RESIDUE BR B 107
10BC1SOFTWAREARG D:17 , ARG D:21BINDING SITE FOR RESIDUE BR D 111
11BC3SOFTWAREGLY A:20 , ILE A:22 , ARG B:3 , PHE B:4BINDING SITE FOR RESIDUE BR A 113
12BC4SOFTWARELYS A:45 , SER B:77 , PRO B:78BINDING SITE FOR RESIDUE BR A 115
13BC5SOFTWARELEU C:87 , GLN C:90BINDING SITE FOR RESIDUE BR C 113
14BC6SOFTWAREARG A:17BINDING SITE FOR RESIDUE BR A 117
15BC7SOFTWARESER A:77 , PRO A:78BINDING SITE FOR RESIDUE BR A 118
16BC8SOFTWARESER A:9BINDING SITE FOR RESIDUE BR A 119
17BC9SOFTWARESER A:9 , ASP A:12BINDING SITE FOR RESIDUE BR A 120
18CC1SOFTWARESER A:16 , ARG A:17 , LYS A:18BINDING SITE FOR RESIDUE BR A 121
19CC2SOFTWARESER C:82 , LYS C:83 , LYS C:86BINDING SITE FOR RESIDUE BR C 114
20CC3SOFTWAREARG A:25 , SER A:26BINDING SITE FOR RESIDUE BR A 122
21CC4SOFTWARESER B:26 , ILE D:27 , GLN D:90BINDING SITE FOR RESIDUE BR D 112
22CC5SOFTWAREARG A:50 , TRP B:7BINDING SITE FOR RESIDUE BR B 108
23CC6SOFTWARESER A:26BINDING SITE FOR RESIDUE BR A 124
24CC7SOFTWAREARG A:96BINDING SITE FOR RESIDUE BR A 125
25CC9SOFTWAREARG C:93 , ARG C:96 , ARG C:97 , SER D:13 , ARG D:14 , ARG D:25BINDING SITE FOR RESIDUE MLI C 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DLU)

(-) 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:95
 aligned with SRP19_PYRFU | Q8TZT9 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:102
                                                                                                                            100   
                                    11        21        31        41        51        61        71        81        91        |-  
          SRP19_PYRFU     2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNPRLSGIDEELRTFGMIVLESPYGKSKSLKLIAQKIREFRRRSA---   -
               SCOP domains d3dlua_ A: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhh...hhhhh............hhhhhhhhhhhh..eeeeeeeeee..-------..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3dlu A   2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNP-------ELRTFGMIVLESPYGKSKSLKLIAQKIREFRRRSAGTL 103
                                    11        21        31        41        51      |  -    |   71        81        91       101  
                                                                                   58      66                                     


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with SRP19_PYRFU | Q8TZT9 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:102
                                                                                                                            100   
                                    11        21        31        41        51        61        71        81        91        |-  
          SRP19_PYRFU     2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNPRLSGIDEELRTFGMIVLESPYGKSKSLKLIAQKIREFRRRSA---   -
               SCOP domains d3dlub_ B: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhh...hhhhh............hhhhhhhhhhhh..eeeeeeeeee..---------.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3dlu B   2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNP---------RTFGMIVLESPYGKSKSLKLIAQKIREFRRRSAGTL 103
                                    11        21        31        41        51      |  -      | 71        81        91       101  
                                                                                   58        68                                   


Chain C from PDB  Type:PROTEIN  Length:88
 aligned with SRP19_PYRFU | Q8TZT9 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:97
                                    11        21        31        41        51        61        71        81        91       
          SRP19_PYRFU     2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNPRLSGIDEELRTFGMIVLESPYGKSKSLKLIAQKIREFRRR  98
               SCOP domains d3dluc_ C: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhh....................hhhhhhhhhhhh..eeeeeeeeee.---------.eeeeeeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3dlu C   2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLN---------LRTFGMIVLESPYGKSKSLKLIAQKIREFRRR  98
                                    11        21        31        41        51     |   -     |  71        81        91       
                                                                                  57        67                               


Chain D from PDB  Type:PROTEIN  Length:87
 aligned with SRP19_PYRFU | Q8TZT9 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:97
                                    11        21        31        41        51        61        71        81        91       
          SRP19_PYRFU     2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNPRLSGIDEELRTFGMIVLESPYGKSKSLKLIAQKIREFRRR  98
               SCOP domains d3dlud_ D: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhh...hhhhh............hhhhhhhhhhhh..eeeeeeeee.----------..eeeeeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3dlu D   2 GRFVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKL----------LRTFGMIVLESPYGKSKSLKLIAQKIREFRRR  98
                                    11        21        31        41        51    |    -     |  71        81        91       
                                                                                 56         67
   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 3DLU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SRP19_PYRFU | Q8TZT9)
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:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0048500    signal recognition particle    A complex of protein and RNA which facilitates translocation of proteins across membranes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SRP19_PYRFU | Q8TZT9: 3dlv

(-) Related Entries Specified in the PDB File

3dlv DIFFERENT CRYSTAL FORM OF SRP19 FROM PYROCOCCUS FURIOSUS
3dm5 DIFFERENT CRYSTAL FORM