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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE
 
Authors :  N. Tanaka, M. Nakanishi, Y. Kusakabe, Y. Goto, Y. Kitade, K. T. Nakamura
Date :  19 May 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Nuclease, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tanaka, M. Nakanishi, Y. Kusakabe, Y. Goto, Y. Kitade, K. T. Nakamura
Structural Basis For Recognition Of 2', 5'-Linked Oligoadenylates By Human Ribonuclease L
Embo J. V. 23 3929 2004
PubMed-ID: 15385955  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600420
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-5A-DEPENDENT RIBONUCLEASE
    ChainsA
    EC Number3.1.26.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 21-305
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym2-5A-DEPENDENT RNASE, RIBONUCLEASE L, RNASE L, RIBONUCLEASE 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
125A1Ligand/Ion5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:55 , GLY A:58 , TRP A:60 , ASN A:65 , GLN A:68 , LYS A:89 , ASP A:122 , TYR A:124 , PHE A:126 , GLU A:131 , TYR A:135 , ARG A:155 , HOH A:1004 , HOH A:1005 , HOH A:1017 , HOH A:1022 , HOH A:1036 , HOH A:1051 , HOH A:1059 , HOH A:1088 , HOH A:1098 , HOH A:1109 , HOH A:1115 , HOH A:1143 , HOH A:1159BINDING SITE FOR RESIDUE 25A A 1001

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:293 -A:301

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013509G59SRN5A_HUMANPolymorphism151296858AG59S
2UniProtVAR_042358I97LRN5A_HUMANPolymorphism56250729AL97L
3UniProtVAR_042359A289TRN5A_HUMANPolymorphism35553278AA289T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 7)

Asymmetric/Biological Unit (2, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.RN5A_HUMAN24-304  1A:24-304
2ANK_REPEATPS50088 Ankyrin repeat profile.RN5A_HUMAN24-56
58-90
91-123
124-156
167-200
201-237
  6A:24-56
A:58-90
A:91-123
A:124-156
A:167-200
A:201-237

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003675591ENSE00001445029chr1:182558391-18255830290RN5A_HUMAN-00--
1.2bENST000003675592bENSE00001445028chr1:182556105-1825544621644RN5A_HUMAN1-4944941A:21-305285
1.3ENST000003675593ENSE00000922066chr1:182553301-18255321686RN5A_HUMAN494-522290--
1.4ENST000003675594ENSE00000922067chr1:182551393-182551188206RN5A_HUMAN523-591690--
1.5ENST000003675595ENSE00000922068chr1:182550492-182550360133RN5A_HUMAN591-635450--
1.6ENST000003675596ENSE00000922069chr1:182545524-182545391134RN5A_HUMAN636-680450--
1.7bENST000003675597bENSE00001818322chr1:182544713-1825427691945RN5A_HUMAN680-741620--

(-) 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:285
 aligned with RN5A_HUMAN | Q05823 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:285
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
           RN5A_HUMAN    21 AAVEDNHLLIKAVQNEDVDLVQQLLEGGANVNFQEEEGGWTPLHNAVQMSREDIVELLLRHGADPVLRKKNGATPFILAAIAGSVKLLKLFLSKGADVNECDFYGFTAFMEAAVYGKVKALKFLYKRGANVNLRRKTKEDQERLRKGGATALMDAAEKGHVEVLKILLDEMGADVNACDNMGRNALIHALLSSDDSDVEAITHLLLDHGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCKRGASTDCGDLV 305
               SCOP domains d1wdya_ A: RNase L, 2-5a-dependent ribonuclease                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1wdyA00 A:21-305  [code=1.25.40.20, no name defined]                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-1wdyA01 A:272-304            - Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-1wdyA02 A:272-304            - Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-1wdyA03 A:272-304            - Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-1wdyA04 A:272-304            - Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-1wdyA05 A:272-304            - Pfam domains (5)
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh..........hhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh....hhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------S-------------------------------------L-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------- SAPs(SNPs)
                PROSITE (1) ---ANK_REPEAT  PDB: A:24-56         -ANK_REPEAT  PDB: A:58-90         ANK_REPEAT  PDB: A:91-123        ANK_REPEAT  PDB: A:124-156       ----------ANK_REPEAT  PDB: A:167-200        ANK_REPEAT  PDB: A:201-237           -------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---ANK_REP_REGION  PDB: A:24-304 UniProt: 24-304                                                                                                                                                                                                                                            - PROSITE (2)
               Transcript 1 Exon 1.2b  PDB: A:21-305 UniProt: 1-494 [INCOMPLETE]                                                                                                                                                                                                                                          Transcript 1
                 1wdy A  21 AAVEDNHLLIKAVQNEDVDLVQQLLEGGANVNFQEEEGGWTPLHNAVQMSREDIVELLLRHGADPVLRKKNGATPFLLAAIAGSVKLLKLFLSKGADVNECDFYGFTAFMEAAVYGKVKALKFLYKRGANVNLRRKTKEDQERLRKGGATALMDAAEKGHVEVLKILLDEMGADVNACDNMGRNALIHALLSSDDSDVEAITHLLLDHGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCKRGASTDCGDLV 305
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: Ank (35)
(-)
Family: Ank (23)
1aAnk-1wdyA01A:272-304
1bAnk-1wdyA02A:272-304
1cAnk-1wdyA03A:272-304
1dAnk-1wdyA04A:272-304
1eAnk-1wdyA05A:272-304

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RN5A_HUMAN | Q05823)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
    GO:0043021    ribonucleoprotein complex binding    Interacting selectively and non-covalently with any complex of RNA and protein.
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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0045444    fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:2001275    positive regulation of glucose import in response to insulin stimulus    Any process that activates or increases the frequency, rate or extent of glucose import in response to insulin stimulus.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    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:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RN5A_HUMAN | Q058234g8k 4g8l 4oau 4oav

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WDY)