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(-) Description

Title :  SOLUTION STRUCTURE OF THE ZF-RANBP DOMAIN OF P53-BINDING PROTEIN MDM4
 
Authors :  H. P. Zhang, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 May 05  (Deposition) - 20 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zf-Ranbp Domain; Mdm4 Protein; P53-Binding Protein Mdm4; Mdm2-Like P53-Binding De Protein; Mdmx Protein; Double Minute 4 Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. P. Zhang, F. Hayashi, S. Yokoyama
Solution Structure Of The Zf-Ranbp Domain Of P53-Binding Protein Mdm4
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MDM4 PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP040809-07
    Expression System Vector TypePLASMID
    FragmentZF-RANBP DOMAIN
    GeneMDM4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymP53-BINDING PROTEIN MDM4, MDM2-LIKE P53-BINDING PROTEIN, MDMX PROTEIN, DOUBLE MINUTE 4 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:14 , CYS A:17 , CYS A:28 , CYS A:31BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CR8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CR8)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RANBP2_2PS50199 Zinc finger RanBP2 type profile.MDM4_HUMAN300-329  1A:8-37
2ZF_RANBP2_1PS01358 Zinc finger RanBP2-type signature.MDM4_HUMAN304-323  1A:12-31

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003671821aENSE00001443738chr1:204485511-204485637127MDM4_HUMAN-00--
1.2aENST000003671822aENSE00002156140chr1:204494612-204494724113MDM4_HUMAN1-26260--
1.3ENST000003671823ENSE00001039934chr1:204495488-20449556275MDM4_HUMAN27-51250--
1.4ENST000003671824ENSE00001039926chr1:204499812-204499945134MDM4_HUMAN52-96450--
1.5aENST000003671825aENSE00001039924chr1:204501319-20450137456MDM4_HUMAN96-115200--
1.8aENST000003671828aENSE00001039927chr1:204506558-20450662568MDM4_HUMAN115-137230--
1.9dENST000003671829dENSE00001039922chr1:204507337-204507436100MDM4_HUMAN138-171340--
1.10bENST0000036718210bENSE00001075004chr1:204511912-204512072161MDM4_HUMAN171-224541A:1-6 (gaps)15
1.11bENST0000036718211bENSE00001074998chr1:204513663-204513812150MDM4_HUMAN225-274500--
1.12bENST0000036718212bENSE00001075005chr1:204515925-20451600581MDM4_HUMAN275-301271A:7-9 (gaps)23
1.13eENST0000036718213eENSE00001123001chr1:204518241-2045272489008MDM4_HUMAN302-4901891A:10-5344

(-) 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:53
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:142
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343  
           MDM4_HUMAN   204 GNLRSNYTPRSNGSTDLQTNQDVGTAIVSDTTDDLWFLNESVSEQLGVGIKVEAADTEQTSEEVGKVSDKKVIEVGKNDDLEDSKSLSDDTDVEVTSEDEWQCTECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSLSTSD 345
               SCOP domains ------------------------------------------------------------------------------------------------d2cr8a1 A:8-48 MDM4                      ----- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---------.....------------------------------------------------------------.--------------------.............................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------ZF_RANBP2_2  PDB: A:8-37      ---------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------ZF_RANBP2_1         ---------------------- PROSITE (2)
               Transcript 1 Exon 1.10b           Exon 1.11b  PDB: - UniProt: 225-274               Exon 1.12b UniProt: 275-301Exon 1.13e  PDB: A:10-53 UniProt: 302-490    Transcript 1
                 2cr8 A   1 G---------SSGSS------------------------------------------------------------G--------------------SEDEWQCTECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSGPSSG  53
                            |        -|   |    -         -         -         -         -         -     |   -         -      | 11        21        31        41        51  
                            |         2   6                                                            7                    8                                             
                            1                                                                                                                                             

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  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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CR8)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (MDM4_HUMAN | O15151)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030330    DNA damage response, signal transduction by p53 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0045023    G0 to G1 transition    The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071456    cellular response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0071157    negative regulation of cell cycle arrest    Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042177    negative regulation of protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
cellular component
    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

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

UniProtKB/Swiss-Prot
        MDM4_HUMAN | O151512mwy 2n06 2n0u 2n0w 2n14 2vje 2vjf 2vyr 3dab 3eqy 3fdo 3fe7 3fea 3jzo 3jzp 3jzq 3lbj 3mqr 3u15 4rxz 5mnj

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