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(-) Description

Title :  STRUCTURE OF PROTEIN L7AE BOUND TO A K-TURN DERIVED FROM AN ARCHAEAL BOX H/ACA SRNA
 
Authors :  T. Hamma, A. Ferre-D'Amare
Date :  13 Feb 04  (Deposition) - 18 May 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein-Rna Complex, Protein-Rna Complex Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hamma, A. Ferre-D'Amare
Structure Of Protein L7Ae Bound To A K-Turn Derived From An Archaeal Box H/Aca Srna At 1. 8 A Resolution.
Structure V. 12 893 2004
PubMed-ID: 15130481  |  Reference-DOI: 10.1016/J.STR.2004.03.015

(-) Compounds

Molecule 1 - BOX H/ACA SRNA
    Chains: D, E, F
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L7AE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B DERIVATIVE
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPL7AE, MJ1203
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2K1Ligand/IonPOTASSIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU F:206 , G F:208 , HOH F:874 , HOH F:953 , HOH F:995 , HOH F:1023 , HOH F:1024BINDING SITE FOR RESIDUE CA F 751
02AC2SOFTWAREU E:206 , G E:208 , HOH E:899 , HOH E:1013 , HOH E:1020 , HOH E:1026BINDING SITE FOR RESIDUE CA E 752
03AC3SOFTWAREA F:205 , U F:206 , U F:207 , G F:208 , HOH F:979BINDING SITE FOR RESIDUE CA F 753
04AC4SOFTWAREA E:205 , U E:206 , U E:207 , G E:208 , HOH E:975BINDING SITE FOR RESIDUE CA E 754
05AC5SOFTWAREU D:206 , G D:208 , HOH D:886 , HOH D:986 , HOH D:987 , HOH D:1030BINDING SITE FOR RESIDUE CA D 755
06AC6SOFTWAREA D:205 , U D:206 , U D:207 , G D:208 , HOH D:987 , HOH D:1033 , HOH E:994BINDING SITE FOR RESIDUE CA D 756
07AC7SOFTWAREA D:212 , HOH D:852 , HOH D:910 , HOH D:956 , HOH D:957 , HOH D:1036BINDING SITE FOR RESIDUE CA D 757
08AC8SOFTWAREA F:212 , HOH F:851 , HOH F:885 , HOH F:1007 , HOH F:1021BINDING SITE FOR RESIDUE CA F 758
09AC9SOFTWAREHOH E:1039BINDING SITE FOR RESIDUE CA E 759
10BC1SOFTWAREHOH F:1040 , HOH F:1041 , HOH F:1042 , HOH F:1043 , HOH F:1078BINDING SITE FOR RESIDUE CA F 760
11BC2SOFTWAREG E:213BINDING SITE FOR RESIDUE K E 761

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:53 -Pro A:54
2Lys B:53 -Pro B:54
3Lys C:53 -Pro C:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L7AEPS01082 Ribosomal protein L7Ae signature.RL7A_METJA65-82
 
 		  3A:65-82
B:65-82
C:65-82

(-) Exons   (0, 0)

(no "Exon" information available for 1SDS)

(-) 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:115
 aligned with RL7A_METJA | P54066 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
           RL7A_METJA     2 AVYVKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLK 116
               SCOP domains d1sdsa_ A: Ribosomal protein L7ae                                                                                   SCOP domains
               CATH domains 1sdsA00 A:2-116  [code=3.30.1330.30, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.eeeehhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------RIBOSOMAL_L7AE    ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1sds A   2 AVYVKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLK 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with RL7A_METJA | P54066 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:109
                                    16        26        36        46        56        66        76        86        96       106         
           RL7A_METJA     7 FKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVL 115
               SCOP domains d1sdsb_ B: Ribosomal protein L7ae                                                                             SCOP domains
               CATH domains 1sdsB00 B:7-115  [code=3.30.1330.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.eeeehhhhhhhhhhh....eeeee....hhhhh.hhhhhhhhhh..eeee.hhhhhhhhh.......eeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------RIBOSOMAL_L7AE    --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1sds B   7 FKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVL 115
                                    16        26        36        46        56        66        76        86        96       106         


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with RL7A_METJA | P54066 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:112
                                    14        24        34        44        54        64        74        84        94       104       114  
           RL7A_METJA     5 VKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLK 116
               SCOP domains d1sdsc_ C: Ribosomal protein L7ae                                                                                SCOP domains
               CATH domains 1sdsC00 C:5-116  [code=3.30.1330.30, no name defined]                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhh....eeeee....hhhhh.hhhhhhhhhh..eeee.hhhhhhhhh.......eeeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------RIBOSOMAL_L7AE    ---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1sds C   5 VKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLK 116
                                    14        24        34        44        54        64        74        84        94       104       114  


Chain D from PDB  Type:RNA  Length:15
                                               
                 1sds D 201 CCUGAUUGGUGAGGG 215
                                   210     


Chain E from PDB  Type:RNA  Length:15
                                               
                 1sds E 201 CCUGAUUGGUGAGGG 215
                                   210     


Chain F from PDB  Type:RNA  Length:15
                                               
                 1sds F 201 CCUGAUUGGUGAGGG 215
                                   210
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (RL7A_METJA | P54066)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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).
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0004526    ribonuclease P activity    Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0000470    maturation of LSU-rRNA    Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    GO:0001682    tRNA 5'-leader removal    Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL7A_METJA | P54066: 1ra4 1xbi 3paf

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