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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SRP19/S-DOMAIN SRP RNA COMPLEX OF SULFOLOBUS SOLFATARICUS
 
Authors :  K. Wild, G. Bange, G. Bozkurt, I. Sinning
Date :  26 Nov 09  (Deposition) - 16 Feb 10  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ribonucleoprotein Complex, Rna-Rna Tertiary Interactions, Asymmetric Loop, 7S Rna, Signal Recognition Particle, Structural Rna, Rna- Binding, Rna-Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wild, G. Bange, G. Bozkurt, B. Segnitz, A. Hendricks, I. Sinning
Structural Insights Into The Assembly Of The Human And Archaeal Signal Recognition Particles.
Acta Crystallogr. , Sect. D V. 66 295 2010
PubMed-ID: 20179341  |  Reference-DOI: 10.1107/S0907444910000879

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SRP19, SSO0165
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: SRP19
 
Molecule 2 - SRP RNA
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: S DOMAIN
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1K4Ligand/IonPOTASSIUM ION
2MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA D:217BINDING SITE FOR RESIDUE K D 1
2AC2SOFTWAREA C:217BINDING SITE FOR RESIDUE K C 2
3AC3SOFTWAREA C:220BINDING SITE FOR RESIDUE K C 3
4AC4SOFTWAREG D:201 , C D:222BINDING SITE FOR RESIDUE K D 4
5AC5SOFTWAREA C:204 , G C:205 , G C:206 , G C:218BINDING SITE FOR RESIDUE MG C 6
6AC6SOFTWAREGLU A:9 , ARG A:11 , ILE A:54BINDING SITE FOR RESIDUE MG A 103
7AC7SOFTWAREC C:156 , C C:202BINDING SITE FOR RESIDUE MG C 8
8AC8SOFTWAREG D:215 , G D:216BINDING SITE FOR RESIDUE MG D 9
9AC9SOFTWAREG C:230BINDING SITE FOR RESIDUE MG C 10

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KTW)

(-) 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:92
 aligned with SRP19_SULSO | Q980W2 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:92
                                    11        21        31        41        51        61        71        81        91  
          SRP19_SULSO     2 SLRDLKEENRIVIWPSYFFSPTRSKGRRLARIPYKIKTEELVSTLRELGLDPIVIENKKYPRDRKINFLIAVKKVKSKNYTLKIIHNALMGT  93
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeee.hhhhhh................hhhhhhhhhhhh....eee.............eeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3ktw A   2 SLRDLKEENRIVIWPSYFFSPTRSKGRRLARIPYKIKTEELVSTLRELGLDPIVIENKKYPRDRKINFLIAVKKVKSKNYTLKIIHNALMGT  93
                                    11        21        31        41        51        61        71        81        91  


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with SRP19_SULSO | Q980W2 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
          SRP19_SULSO     2 SLRDLKEENRIVIWPSYFFSPTRSKGRRLARIPYKIKTEELVSTLRELGLDPIVIENKKYPRDRKINFLIAVKKVKSKNYTLKIIHNALMGTR  94
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------SRP19-3ktwB01 B:12-94                                                               Pfam domains (1)
           Pfam domains (2) ----------SRP19-3ktwB02 B:12-94                                                               Pfam domains (2)
         Sec.struct. author .hhhhhh..eeee.hhhhhh................hhhhhhhhhhhh....eee....hhhhh....eeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3ktw B   2 SLRDLKEENRIVIWPSYFFSPTRSKGRRLARIPYKIKTEELVSTLRELGLDPIVIENKKYPRDRKINFLIAVKKVKSKNYTLKIIHNALMGTR  94
                                    11        21        31        41        51        61        71        81        91   


Chain C from PDB  Type:RNA  Length:96
                                                                                                                                
                 3ktw C 141 AGAUAGUCGUGGGUUCCCUUUCUGGAGGGAGAGGGAAUUCCACGUUGACCGGGGGAACCGGCCAGGCCCGGAAGGGAGCAACCGUGCCCGGCUAUC 236
                                   150       160       170       180       190       200       210       220       230      


Chain D from PDB  Type:RNA  Length:95
                                                                                                                               
                 3ktw D 141 AGAUAGUCGUGGGUUCCCUUUCUGGAGGGAGAGGGAAUUCCACGUUGACCGGGGGAACCGGCCAGGCCCGGAAGGGAGCAACCGUGCCCGGCUAU 235
                                   150       160       170       180       190       200       210       220       230
   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 3KTW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: SRP19] (9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SRP19_SULSO | Q980W2)
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 Specified in the PDB File

3ktv THE SAME COMPLEX FOR HOMO SAPIENS