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(-) Description

Title :  STRUCTURE OF THE RIBONUCLEOPROTEIN CORE OF THE E. COLI SIGNAL RECOGNITION PARTICLE
 
Authors :  R. T. Batey, R. P. Rambo, L. Lucast, B. Rha, J. Doudna
Date :  17 Jan 00  (Deposition) - 28 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Double Helix, Tetraloop, Internal Loop, Signal Recognition Particle, Srp, Ribonucleoprotein, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. T. Batey, R. P. Rambo, L. Lucast, B. Rha, J. A. Doudna
Crystal Structure Of The Ribonucleoprotein Core Of The Signal Recognition Particle.
Science V. 287 1232 2000
PubMed-ID: 10678824  |  Reference-DOI: 10.1126/SCIENCE.287.5456.1232
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4.5 S RNA DOMAIN IV
    ChainsB
    EngineeredYES
    Fragment4.5S RNA FRAGMENT (RESIDUES 32-74)
    MutationYES
    SyntheticYES
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE PROTEIN (FIFTY-FOUR HOMOLOG)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC TERMINAL DOMAIN (RESIDUES 328-432)
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymFFH-M DOMAIN, P48

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2K3Ligand/IonPOTASSIUM ION
3MG4Ligand/IonMAGNESIUM ION
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU B:146 , C B:147 , A B:164 , G B:165 , HOH B:816 , HOH B:842BINDING SITE FOR RESIDUE K B 701
2AC2SOFTWAREU B:135 , G B:136 , U B:137 , HOH B:833 , HOH B:855 , HOH B:893 , HOH B:908 , HOH B:1028BINDING SITE FOR RESIDUE K B 702
3AC3SOFTWAREGLY A:57 , G B:149 , G B:150 , G B:162 , C B:163BINDING SITE FOR RESIDUE K B 703
4AC4SOFTWAREHOH B:810 , HOH B:820 , HOH B:826 , HOH B:832 , HOH B:881 , HOH B:882BINDING SITE FOR RESIDUE MG B 801
5AC5SOFTWAREC B:141 , HOH B:817 , HOH B:845 , HOH B:883 , HOH B:884 , HOH B:885BINDING SITE FOR RESIDUE MG B 802
6AC6SOFTWAREG B:149 , HOH B:806 , HOH B:886 , HOH B:887 , HOH B:888 , HOH B:889BINDING SITE FOR RESIDUE MG B 803
7AC7SOFTWAREHOH B:835 , HOH B:865 , HOH B:870 , HOH B:890 , HOH B:891 , HOH B:892BINDING SITE FOR RESIDUE MG B 804

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DUL)

(-) 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:69
 aligned with SRP54_ECO57 | P0AGD9 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:102
                                   338       348       358       368       378       388       398       408       418       428  
          SRP54_ECO57   329 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKM 430
               SCOP domains d1dula_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 1dulA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1dul A   1 FDLNDFLEQ---------------------------------KVLVRmEAIINSmTmKERAKPEIIKGSRKRRIAAGSGmQVQDVNRLLKQFDDmQRmmKKm  82
                                    |-         -         -         -  |    |30    | | 40        50        60        70    |  |80 |
                                    9                                23    |     35-MSE                   60-MSE         75-MSE  |
                                                                          28-MSE   37-MSE                                   78-MSE
                                                                                                                             79-MSE
                                                                                                                                82-MSE

Chain A from PDB  Type:PROTEIN  Length:69
 aligned with SRP54_ECOL6 | P0AGD8 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:102
                                   338       348       358       368       378       388       398       408       418       428  
          SRP54_ECOL6   329 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKM 430
               SCOP domains d1dula_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 1dulA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1dul A   1 FDLNDFLEQ---------------------------------KVLVRmEAIINSmTmKERAKPEIIKGSRKRRIAAGSGmQVQDVNRLLKQFDDmQRmmKKm  82
                                    |-         -         -         -  |    |30    | | 40        50        60        70    |  |80 |
                                    9                                23    |     35-MSE                   60-MSE         75-MSE  |
                                                                          28-MSE   37-MSE                                   78-MSE
                                                                                                                             79-MSE
                                                                                                                                82-MSE

Chain A from PDB  Type:PROTEIN  Length:69
 aligned with SRP54_ECOLI | P0AGD7 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:102
                                   338       348       358       368       378       388       398       408       418       428  
          SRP54_ECOLI   329 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKM 430
               SCOP domains d1dula_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 1dulA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1dul A   1 FDLNDFLEQ---------------------------------KVLVRmEAIINSmTmKERAKPEIIKGSRKRRIAAGSGmQVQDVNRLLKQFDDmQRmmKKm  82
                                    |-         -         -         -  |    |30    | | 40        50        60        70    |  |80 |
                                    9                                23    |     35-MSE                   60-MSE         75-MSE  |
                                                                          28-MSE   37-MSE                                   78-MSE
                                                                                                                             79-MSE
                                                                                                                                82-MSE

Chain B from PDB  Type:RNA  Length:49
                                                                                 
                 1dul B 130 GGCUCUGUUUACCAGGUCAGGUCCGAAAGGAAGCAGCCAAGGCAGAGCc 178
                                   139       149       159       169        |
                                                                          178-CCC

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRP54_ECOLI | P0AGD7)
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0048500    signal recognition particle    A complex of protein and RNA which facilitates translocation of proteins across membranes.

Chain A   (SRP54_ECO57 | P0AGD9)
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:0048500    signal recognition particle    A complex of protein and RNA which facilitates translocation of proteins across membranes.

Chain A   (SRP54_ECOL6 | P0AGD8)
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: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
        SRP54_ECO57 | P0AGD91hq1
        SRP54_ECOL6 | P0AGD81hq1
        SRP54_ECOLI | P0AGD71hq1 2j28 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv 2xkv 2xxa 3lqx 4c7o 5aka 5gad 5gaf 5gag 5gah

(-) Related Entries Specified in the PDB File

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