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(-) Description

Title :  STRUCTURE OF C-TERMINAL REGION OF ACIDIC P2 RIBOSOMAL PROTEIN COMPLEXED WITH TRICHOSANTHIN
 
Authors :  P. H. Too, A. N. Mak, G. Zhu, S. W. Au, K. B. Wong, P. C. Shaw
Date :  11 Jan 07  (Deposition) - 05 Feb 08  (Release) - 10 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ribosome Inactiviating Protein, Ribosomal Protein, Protein Synthesis Inhibitor, Toxin, Hydrolase, Plant Defense, Antiviral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. H. Too, M. K. Ma, A. N. Mak, Y. T. Wong, C. K. Tung, G. Zhu, S. W. Au, K. B. Wong, P. C. Shaw
The C-Terminal Fragment Of The Ribosomal P Protein Complexed To Trichosanthin Reveals The Interaction Between The Ribosome-Inactivating Protein And The Ribosome.
Nucleic Acids Res. V. 37 602 2009
PubMed-ID: 19073700  |  Reference-DOI: 10.1093/NAR/GKN922

(-) Compounds

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
    ChainsA, B
    EC Number3.2.2.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3D
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentRESIDUES 25-270
    Organism CommonMONGOLIAN SNAKE-GOURD
    Organism ScientificTRICHOSANTHES KIRILOWII
    Organism Taxid3677
    SynonymRRNA N-GLYCOSIDASE, ALPHA-TCS, TRICHOSANTHIN
 
Molecule 2 - ACIDIC RIBOSOMAL PROTEIN P2
    ChainsC, D
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2JDL)

(-) Sites  (0, 0)

(no "Site" information available for 2JDL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPT_TRIKI178-194
 
  2A:155-171
B:155-171
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPT_TRIKI178-194
 
  1A:155-171
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPT_TRIKI178-194
 
  1-
B:155-171

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003211531aENSE00001318871chr11:809647-810039393RLA2_HUMAN-00--
1.1eENST000003211531eENSE00001296345chr11:810234-810357124RLA2_HUMAN1-41410--
1.3bENST000003211533bENSE00001262054chr11:811597-81164549RLA2_HUMAN42-58170--
1.4bENST000003211534bENSE00001262045chr11:812535-81263399RLA2_HUMAN58-91340--
1.5eENST000003211535eENSE00001296767chr11:812760-812875116RLA2_HUMAN91-115252C:2-11
D:3-11
10
9

(-) 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:247
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:247
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
           RIPT_TRIKI    24 DVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 270
               SCOP domains d2jdla_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains 2jdlA01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       2jdlA02 A:163-247 Ricin (A Subunit), domain 2                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jdl A   1 MVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:247
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
           RIPT_TRIKI    24 DVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 270
               SCOP domains d2jdlb_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains 2jdlB01 B:1-162 Ricin (A subunit), domain 1                                                                                                                       2jdlB02 B:163-247 Ricin (A Subunit), domain 2                                         CATH domains
           Pfam domains (1) --RIP-2jdlB01 B:3-202                                                                                                                                                                                     --------------------------------------------- Pfam domains (1)
           Pfam domains (2) --RIP-2jdlB02 B:3-202                                                                                                                                                                                     --------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eee....hhhhhhhhhhhhhh...eeeee..eeee.........eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jdl B   1 MVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with RLA2_HUMAN | P05387 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:10
                                   115
           RLA2_HUMAN   106 DDDMGFGLFD 115
               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 1 Exon 1.5e  Transcript 1
                 2jdl C   2 DDDMGFGLFD  11
                                    11

Chain D from PDB  Type:PROTEIN  Length:9
 aligned with RLA2_HUMAN | P05387 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:9
           RLA2_HUMAN   107 DDMGFGLFD 115
               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 1 Exon 1.5e Transcript 1
                 2jdl D   3 DDMGFGLFD  11

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RIPT_TRIKI | P09989)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030598    rRNA N-glycosylase activity    Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

Chain C,D   (RLA2_HUMAN | P05387)
molecular function
    GO:0070180    large ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
    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:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
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:0002181    cytoplasmic translation    The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    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.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    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:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030687    preribosome, large subunit precursor    A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit.
    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
        RIPT_TRIKI | P099891gis 1giu 1j4g 1mrj 1mrk 1nli 1qd2 1tcs 2jjr 2vs6
        RLA2_HUMAN | P053871s4j 2lbf 2w1o 4beh 4v6x 5ddz 5gu4

(-) Related Entries Specified in the PDB File

1gis A TRICHOSANTHIN(TCS) MUTANT(E85Q) COMPLEX STRUCTURE WITH 2'-DEOXY-ADENOSIN-5'- MONOPHOSPHATE
1giu A TRICHOSANTHIN(TCS) MUTANT(E85R) COMPLEX STRUCTURE WITHADENINE
1j4g CRYSTAL STRUCTURE ANALYSIS OF THE TRICHOSANTHIN DELTA C7
1mrj ALPHA-TRICHOSANTHIN COMPLEXED WITH ADENINE
1mrk ALPHA-TRICHOSANTHIN COMPLEXED WITH FORMYCIN
1nli COMPLEX OF [E160A-E189A] TRICHOSANTHIN AND ADENINE
1qd2 CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG
1tcs TRICHOSANTHIN COMPLEXED WITH NADPH