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(-) Description

Title :  STRUCTURAL BASIS FOR SPECIFIC SUBSTRATE RECOGNITION BY THE CHLOROPLAST SIGNAL RECOGNITION PARTICLE PROTEIN CPSRP43
 
Authors :  I. Holdermann, K. F. Stengel, K. Wild, I. Sinning
Date :  10 Jun 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chloroplast Srp System, Signal Recognition Particle, Signal Sequence, Ankyrin Repeat, Chromodomain, Type I Turn, Substrate Protein Recognition, L18 Region, Lhcp, Ank Repeat, Chloroplast, Coiled Coil, Plastid, Ribonucleoprotein, Protein Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. F. Stengel, I. Holdermann, P. Cain, C. Robinson, K. Wild, I. Sinning
Structural Basis For Specific Substrate Recognition By The Chloroplast Signal Recognition Particle Protein Cpsrp43.
Science V. 321 253 2008
PubMed-ID: 18621669  |  Reference-DOI: 10.1126/SCIENCE.1158640
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 43 KDA PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 85-267
    GeneCAO, AT2G47450, T30B22.25
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymCHROMO PROTEIN SRP43, CPSRP43
 
Molecule 2 - YPGGSFDPLGLA
    ChainsB
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SynonymLHCP L18 REGION
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:118 , ARG A:206 , PRO A:207 , GLU A:208BINDING SITE FOR RESIDUE CL A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.SR43C_ARATH152-234  1A:152-234
2ANK_REPEATPS50088 Ankyrin repeat profile.SR43C_ARATH159-191
193-225
  2A:159-191
A:193-225

(-) Exons   (0, 0)

(no "Exon" information available for 3DEP)

(-) 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:183
 aligned with SR43C_ARATH | O22265 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:183
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   
          SR43C_ARATH    85 EVNKIIGSRTAGEGAMEYLIEWKDGHSPSWVPSSYIAADVVSEYETPWWTAARKADEQALSQLLEDRDVDAVDENGRTALLFVAGLGSDKCVRLLAEAGADLDHRDMRGGLTALHMAAGYVRPEVVEALVELGADIEVEDERGLTALELAREILKTTPKGNPMQFGRRIGLEKVINVLEGQVF 267
               SCOP domains d3depa1 A:85-128 CpSRP43                    -d3depa2 A:130-218 automated matches                                                      ------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee...eeeeeeee......eeee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------ANK_REP_REGION  PDB: A:152-234 UniProt: 152-234                                    --------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------ANK_REPEAT  PDB: A:159-191       -ANK_REPEAT  PDB: A:193-225       ------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dep A  85 EVNKIIGSRTAGEGAMEYLIEWKDGHSPSWVPSSYIAADVVSEYETPWWTAARKADEQALSQLLEDRDVDAVDENGRTALLFVAGLGSDKCVRLLAEAGADLDHRDMRGGLTALHMAAGYVRPEVVEALVELGADIEVEDERGLTALELAREILKTTPKGNPMQFGRRIGLEKVINVLEGQVF 267
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   

Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3dep B 156 YPGGSFDPLGLA 167
                                   165  

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SR43C_ARATH | O22265)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0045038    protein import into chloroplast thylakoid membrane    The import of proteins into the chloroplast thylakoid membranes. Proteins that are destined for the thylakoid lumen require two uptake-targeting sequences: the first targets the protein to the stroma, and the second targets the protein from the stroma to the thylakoid lumen. Four separate thylakoid-import systems deal with the proteins once they are in the stroma.
    GO:0009644    response to high light intensity    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 high light intensity stimulus.
    GO:0009416    response to light stimulus    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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009941    chloroplast envelope    The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0080085    signal recognition particle, chloroplast targeting    A complex consisting of a protein and RNA component which binds the signal sequence of some proteins and facilitates their export to the chloroplast.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SR43C_ARATH | O222651x32 1x3p 1x3q 2hug 2n88 3deo 3ui2 5e4w 5e4x

(-) Related Entries Specified in the PDB File

3deo