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(-) Description

Title :  VARIANT 4 OF RIBONUCLEOPROTEIN CORE OF THE E. COLI SIGNAL RECOGNITION PARTICLE
 
Authors :  A. Y. Keel, R. P. Rambo, R. T. Batey, J. S. Kieft
Date :  14 May 07  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gu Pair, Hexamine, Rna Phasing, Rna, Cation Binding, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Y. Keel, R. P. Rambo, R. T. Batey, J. S. Kieft
A General Strategy To Solve The Phase Problem In Rna Crystallography.
Structure V. 15 761 2007
PubMed-ID: 17637337  |  Reference-DOI: 10.1016/J.STR.2007.06.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(PLYSS)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C TERMINAL DOMAIN (RESIDUES 328-432)
    Gene: FFH
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FIFTY-FOUR HOMOLOG, P48
 
Molecule 2 - 4.5 S RNA
    Chains: B
    Engineered: YES
    Fragment: DOMAIN IV
    Mutation: YES
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NCO7Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:136 , U B:137 , U B:138 , A B:169 , G B:170 , G B:171BINDING SITE FOR RESIDUE NCO B 201
2AC2SOFTWAREG B:144 , G B:145 , U B:146 , C B:163 , A B:164BINDING SITE FOR RESIDUE NCO B 202
3AC3SOFTWAREA B:148 , G B:149 , G B:150 , U B:151BINDING SITE FOR RESIDUE NCO B 203
4AC4SOFTWAREG B:154 , A B:156BINDING SITE FOR RESIDUE NCO B 204
5AC5SOFTWAREG B:158 , G B:159BINDING SITE FOR RESIDUE NCO B 205
6AC6SOFTWAREU B:146 , C B:147 , A B:161 , G B:162BINDING SITE FOR RESIDUE NCO B 206
7AC7SOFTWAREG B:131 , G B:132 , U B:133 , G B:174 , G B:175 , U B:176 , C B:177BINDING SITE FOR RESIDUE NCO B 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PXE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PXE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PXE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PXE)

(-) Exons   (0, 0)

(no "Exon" information available for 2PXE)

(-) 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_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 d2pxea_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 2pxeA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains SRP_SPB-2                                 pxeA01 A:1-79                                            --- Pfam domains
         Sec.struct. author .hhhhhhh.---------------------------------hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2pxe 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
                                                                                 
                 2pxe B 130 GGGUCUGUUUACCAGGUCAGGUCCGAAAGGAAGCAGCCAAGGCAGGUCC 178
                                   139       149       159       169
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (11, 11)

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: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
        SRP54_ECOLI | P0AGD7: 1dul 1hq1 2j28 2pxb 2pxd 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv 2xkv 2xxa 3lqx 4c7o 5aka 5gad 5gaf 5gag 5gah

(-) Related Entries Specified in the PDB File

1dul ORIGINAL STRUCTURE SOLVED BY BATEY, ET AL