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(-) Description

Title :  SOLUTION STRUCTURE OF THE RING FINGER OF HUMAN RETINOBLASTOMA-BINDING PROTEIN 6
 
Authors :  H. Abe, K. Miyamoto, N. Tochio, T. Tomizawa, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Apr 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  P53-Associated Cellular Protein Of Testis, Proliferation Potential-Related Protein, Protein P2P-R, Retinoblastoma- Binding Q Protein 1, Protein Rbq-1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Abe, K. Miyamoto, N. Tochio, T. Tomizawa, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama
Solution Structure Of The Ring Finger Of Human Retinoblastoma-Binding Protein 6
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOBLASTOMA-BINDING PROTEIN 6
    ChainsA
    EngineeredYES
    Expression System PlasmidP060731-05
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 249-309, C3HC4 DOMAIN
    GeneRBBP6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymP53-ASSOCIATED CELLULAR PROTEIN OF TESTIS, PROLIFERATION POTENTIAL-RELATED PROTEIN, PROTEIN P2P-R, RETINOBLASTOMA-BINDING Q PROTEIN 1, PROTEIN RBQ-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:18 , ILE A:20 , CYS A:21 , ASP A:23 , CYS A:39BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREILE A:31 , CYS A:33 , CYS A:34BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.RBBP6_HUMAN259-300  1A:18-59

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003197151bENSE00001944481chr16:24551516-24552113598RBBP6_HUMAN1-56560--
1.2ENST000003197152ENSE00001732323chr16:24557484-24557583100RBBP6_HUMAN56-89340--
1.3aENST000003197153aENSE00001690982chr16:24560266-2456030237RBBP6_HUMAN89-101130--
1.4ENST000003197154ENSE00001733675chr16:24564834-2456487845RBBP6_HUMAN102-116150--
1.5ENST000003197155ENSE00001654475chr16:24566936-2456702489RBBP6_HUMAN117-146300--
1.6ENST000003197156ENSE00001627030chr16:24567142-2456723897RBBP6_HUMAN146-178330--
1.7ENST000003197157ENSE00001655617chr16:24567629-24567768140RBBP6_HUMAN179-225470--
1.8ENST000003197158ENSE00001593165chr16:24570826-24570998173RBBP6_HUMAN225-283591A:1-42 (gaps)53
1.9ENST000003197159ENSE00001650552chr16:24572933-24573036104RBBP6_HUMAN283-317351A:42-6827
1.10ENST0000031971510ENSE00001676101chr16:24573145-24573482338RBBP6_HUMAN318-4301131A:69-74 (gaps)7
1.11ENST0000031971511ENSE00001646664chr16:24574520-2457461697RBBP6_HUMAN430-462330--
1.12ENST0000031971512ENSE00001712710chr16:24574744-2457482279RBBP6_HUMAN463-489270--
1.13ENST0000031971513ENSE00001694672chr16:24574931-2457498555RBBP6_HUMAN489-507190--
1.14ENST0000031971514ENSE00001776080chr16:24576118-2457618669RBBP6_HUMAN507-530240--
1.15ENST0000031971515ENSE00001738863chr16:24578464-24578826363RBBP6_HUMAN530-6511220--
1.16ENST0000031971516ENSE00001745967chr16:24579113-24579214102RBBP6_HUMAN651-685350--
1.17ENST0000031971517ENSE00001175524chr16:24580066-245818201755RBBP6_HUMAN685-12705860--
1.18bENST0000031971518bENSE00001856595chr16:24582197-245841841988RBBP6_HUMAN1270-17925230--

(-) Sequences/Alignments

NMR Structure
   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:74
 aligned with RBBP6_HUMAN | Q7Z6E9 from UniProtKB/Swiss-Prot  Length:1792

    Alignment length:175
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400     
          RBBP6_HUMAN   231 GKKEKPPFLPEEPSSSSEEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNNFKNETGYTKRLRKQLPPPPPPIPPPRPLIQRNLQPLMRSPISRQQDPLMIPVTSSSTHPAPSISSLTSNQSSLAPPVSGNPSSA 405
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------zf-C3HC4_2-2yurA01 A:14-60                     -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------...........hhhhh...........ee......ee..hhhhhhhhhh..................-----------------------------------------------------------------------------------------..-.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------ZF_RING_2  PDB: A:18-59 UniProt: 259-300  --------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:1-42 (gaps) UniProt: 225-283        ----------------------------------Exon 1.10  PDB: A:69-74 (gaps) UniProt: 318-430 [INCOMPLETE]                             Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.9  PDB: A:42-68 [INCOMPLETE]---------------------------------------------------------------------------------------- Transcript 1 (2)
                 2yur A   1 G-----------SSGSSGEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDAL-----------------------------------------------------------------------------------------SG-PSSG  74
                            |        -  |      9        19        29        39        49        59        |-         -         -         -         -         -         -         -         -        70 |   
                            |           2                                                                68                                                                                        69| |   
                            1                                                                                                                                                                       70 |   
                                                                                                                                                                                                      71   

   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 2YUR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YUR)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RING (39)

(-) Gene Ontology  (25, 25)

NMR Structure(hide GO term definitions)
Chain A   (RBBP6_HUMAN | Q7Z6E9)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0061053    somite development    The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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        RBBP6_HUMAN | Q7Z6E92c7h 2ysa 3ztg

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