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(-) Description

Title :  CRYSTAL STRUCTURE OF PERCHLORIC ACID SOLUBLE PROTEIN-A TRANSLATIONAL INHIBITOR
 
Authors :  K. Djinovic Carugo, T. Oka
Date :  12 Mar 99  (Deposition) - 09 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  B  (3x)
Biol. Unit 3:  A  (3x)
Keywords :  Alpha-Beta Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Djinovic Carugo, T. Oka
Crystal Structure Of Perchloric Acid Soluble Protein-A Translational Inhibitor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PERCHLORIC ACID SOLUBLE PROTEIN
    ChainsA, B
    OrganLIVER, KIDNEY
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (3x) B
Biological Unit 3 (3x)A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QAH)

(-) Sites  (0, 0)

(no "Site" information available for 1QAH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QAH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RIDA_RAT105-123
 
  2A:104-122
B:104-122
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RIDA_RAT105-123
 
  2A:104-122
B:104-122
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RIDA_RAT105-123
 
  3-
B:104-122
Biological Unit 3 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RIDA_RAT105-123
 
  3A:104-122
-

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000074301ENSRNOE00000051447chr7:69944267-69944149119RIDA_RAT1-22222A:1-21
B:1-21
21
21
1.2ENSRNOT000000074302ENSRNOE00000051686chr7:69935087-69934982106RIDA_RAT22-57362A:21-56
B:21-56
36
36
1.3ENSRNOT000000074303ENSRNOE00000051862chr7:69934199-6993414555RIDA_RAT58-76192A:57-75
B:57-75
19
19
1.4ENSRNOT000000074304ENSRNOE00000052046chr7:69933374-6993330669RIDA_RAT76-99242A:75-98
B:75-98
24
24
1.5ENSRNOT000000074305ENSRNOE00000052256chr7:69932074-6993201956RIDA_RAT99-117192A:98-116
B:98-116
19
19
1.6ENSRNOT000000074306ENSRNOE00000227477chr7:69930949-69930466484RIDA_RAT118-137202A:117-132
B:117-132
16
16

(-) 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:132
 aligned with RIDA_RAT | P52759 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  
             RIDA_RAT     2 SSIIRKVISTSKAPAAIGAYSQAVLVDRTIYVSGQIGMDPSSGQLVPGGVAEEAKQALKNLGEILKAAGCDFTNVVKTTVLLADINDFGTVNEIYKTYFQGNLPARAAYQVAALPKGSRIEIEAIAVQGPFT 133
               SCOP domains d1qaha_ A: 14.5 kda translational inhibitor protein, L-PSP                                                                           SCOP domains
               CATH domains 1qahA00 A:1-132  [code=3.30.1330.40, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..............eeee..eeeeeee..............hhhhhhhhhhhhhhhhhh....hhheeeeeeee..hhhhhhhhhhhh........eeeeee....hhh..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------UPF0076            ---------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-21-----------------------------------Exon 1.3           ----------------------Exon 1.5           Exon 1.6         Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2  PDB: A:21-56              ------------------Exon 1.4  PDB: A:75-98  ---------------------------------- Transcript 1 (2)
                 1qah A   1 SSIIRKVISTSKAPAAIGAYSQAVLVDRTIYVSGQIGMDPSSGQLVPGGVAEEAKQALKNLGEILKAAGCDFTNVVKTTVLLADINDFGTVNEIYKTYFQGNLPARAAYQVAALPKGSRIEIEAIAVQGPFT 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with RIDA_RAT | P52759 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  
             RIDA_RAT     2 SSIIRKVISTSKAPAAIGAYSQAVLVDRTIYVSGQIGMDPSSGQLVPGGVAEEAKQALKNLGEILKAAGCDFTNVVKTTVLLADINDFGTVNEIYKTYFQGNLPARAAYQVAALPKGSRIEIEAIAVQGPFT 133
               SCOP domains d1qahb_ B: 14.5 kda translational inhibitor protein, L-PSP                                                                           SCOP domains
               CATH domains 1qahB00 B:1-132  [code=3.30.1330.40, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..............eeee..eeeeeeee.............hhhhhhhhhhhhhhhhhh....hhheeeeeeee..hhhhhhhhhhhh........eeeeee....hhh..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------UPF0076            ---------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-21-----------------------------------Exon 1.3           ----------------------Exon 1.5           Exon 1.6         Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2  PDB: B:21-56              ------------------Exon 1.4  PDB: B:75-98  ---------------------------------- Transcript 1 (2)
                 1qah B   1 SSIIRKVISTSKAPAAIGAYSQAVLVDRTIYVSGQIGMDPSSGQLVPGGVAEEAKQALKNLGEILKAAGCDFTNVVKTTVLLADINDFGTVNEIYKTYFQGNLPARAAYQVAALPKGSRIEIEAIAVQGPFT 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  

   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RIDA_RAT | P52759)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016892    endoribonuclease activity, producing 3'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 3'-phosphomonoesters.
    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:0043167    ion binding    Interacting selectively and non-covalently with ions, charged atoms or groups of atoms.
    GO:0036041    long-chain fatty acid binding    Interacting selectively and non-covalently with a long-chain fatty acid. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:1904012    platinum binding    Interacting selectively and non-covalently with platinum.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
    GO:1904013    xenon atom binding    Interacting selectively and non-covalently with xenon atom.
biological process
    GO:0070314    G1 to G0 transition    A cell cycle arrest process that results in arrest during G1 phase, whereupon the cell enters a specialized resting state known as G0 or quiescence.
    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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0050680    negative regulation of epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0033993    response to lipid    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 lipid stimulus.
    GO:1902074    response to salt    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 salt stimulus.
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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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