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(-) Description

Title :  CRYSTAL STRUCTURE OF A SIGNAL SEQUENCE BOUND TO THE SIGNAL RECOGNITION PARTICLE
 
Authors :  T. Hainzl, S. Huang, E. Sauer-Eriksson
Date :  07 Jun 10  (Deposition) - 23 Feb 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,D#,M
Biol. Unit 1:  A,B,M  (1x)
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Protein-Rna Complex, Signal Recognition Particle, Signal Sequence, Ribonucleoprotein, Signaling Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hainzl, S. Huang, G. Merilainen, K. Brannstrom, A. E. Sauer-Eriksson
Structural Basis Of Signal-Sequence Recognition By The Signal Recognition Particle.
Nat. Struct. Mol. Biol. V. 18 389 2011
PubMed-ID: 21336278  |  Reference-DOI: 10.1038/NSMB.1994

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ1034, SRP19
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: SRP19
 
Molecule 2 - SIGNAL RECOGNITION 54 KDA PROTEIN
    Chains: B
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Plasmid: PNZ8048
    Expression System Taxid: 1358
    Expression System Vector Type: PLASMID
    Gene: MJ0101, SRP54
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: SRP54
 
Molecule 3 - SRP RNA
    Chains: M
    Engineered: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII DSM 2661
    Organism Taxid: 243232
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABD#M
Biological Unit 1 (1x): AB M
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:69 , ILE B:108 , GLY B:110 , SER B:111 , GLY B:112 , LYS B:113 , THR B:114 , ARG B:140BINDING SITE FOR RESIDUE PO4 D 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_METJA268-281  1B:268-281
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_METJA268-281  1B:268-281

(-) Exons   (0, 0)

(no "Exon" information available for 3NDB)

(-) 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:PROTEIN  Length:87
 aligned with SRP19_METJA | Q58440 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
          SRP19_METJA     1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN  87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains SRP19-3ndbA01 A:1-87                                                                    Pfam domains
         Sec.struct. author .eehhhhhh...hhhhh............hhhhhhhhhhhh.....ee....hhhhh.....eee.....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3ndb A   1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN  87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:420
 aligned with SRP54_METJA | Q57565 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:447
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       
          SRP54_METJA     2 LDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGGAMPKELSHLTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLRKGKMLRIGGPLGQIMRQLMF 448
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---SRP54_N-3ndbB02 B:5-82                                                        -----------------SRP54-3ndbB01 B:100-295                                                                                                                                                                             -----------------------------SRP_SPB-3ndbB03 B                       :325-424                                                    ------    -------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...............eeeee.....hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh....eeeee..........hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh...eeeee.......eee.hhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhh..-----------------------.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......----..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndb B   2 MDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENM-----------------------LTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLRKG----LALALLLLLLALAL 455
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341         -         -   |   371       381       391       401       411       421        |-   |   448       
                                                                                                                                                                                                                                                                                                                                                                             341                     365                                                              430  442             


Chain M from PDB  Type:RNA  Length:136
                                                                                                                                                                        
                 3ndb M 123 GUCUCGUCCCGUGGGGCUCGGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCGGCGCUCACGGGGGUGCGGGAC 258
                                   132       142       152       162       172       182       192       202       212       222       232       242       252
   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 3NDB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (4, 4)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: SRP19] (9)
(-)
Clan: no clan defined [family: SRP54_N] (20)
(-)
Clan: no clan defined [family: SRP_SPB] (20)

(-) Gene Ontology  (10, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (SRP19_METJA | Q58440)
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.

Chain B   (SRP54_METJA | Q57565)
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: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: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.
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_METJA | Q58440: 1l9a 1lng 2v3c 4xco
        SRP54_METJA | Q57565: 2v3c 4xco

(-) Related Entries Specified in the PDB File

2v3c CRYSTAL STRUCTURE OF THE STP54-SRP19-7S.S SRP RNA COMPLEX OF M. JANNASCHII