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(-) Description

Title :  CRYSTAL STRUCTURE OF THE USP8 INTERACTION DOMAIN OF HUMAN NRDP1
 
Authors :  J. R. Walker, G. V. Avvakumov, S. Xue, E. M. Newman, C. Butler-Cole, P. J. Jr. , J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkare Paganon, Structural Genomics Consortium (Sgc)
Date :  10 Feb 06  (Deposition) - 28 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A
Keywords :  E3 Ligase, Protein Ubiquitination, Structural Genomics, Structural Genomics Consortium, Sgc, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. V. Avvakumov, J. R. Walker, S. Xue, P. J. Finerty Jr. , F. Mackenzie, E. M. Newman, S. Dhe-Paganon
Amino-Terminal Dimerization, Nrdp1-Rhodanese Interaction, And Inhibited Catalytic Domain Conformation Of The Ubiquitin-Specific Protease 8 (Usp8).
J. Biol. Chem. V. 281 38061 2006
PubMed-ID: 17035239  |  Reference-DOI: 10.1074/JBC.M606704200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RING FINGER PROTEIN 41 ISOFORM 1
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUSP8 INTERACTION DOMAIN
    GeneRNF41
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNRDP1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2FZP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:303 -Pro A:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FZP)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003450931bENSE00001517253chr12:56615704-56615544161RNF41_HUMAN-00--
1.2ENST000003450932ENSE00001343359chr12:56610397-56610213185RNF41_HUMAN-00--
1.3ENST000003450933ENSE00002166183chr12:56607854-56607742113RNF41_HUMAN1-30300--
1.5ENST000003450935ENSE00001805618chr12:56604352-56604081272RNF41_HUMAN31-121910--
1.6ENST000003450936ENSE00001274782chr12:56602082-56601947136RNF41_HUMAN121-166460--
1.7ENST000003450937ENSE00001274776chr12:56601533-56601430104RNF41_HUMAN167-201351A:184-20118
1.8ENST000003450938ENSE00001274827chr12:56600582-565982882295RNF41_HUMAN201-3171171A:201-317117

(-) 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:134
 aligned with RNF41_HUMAN | Q9H4P4 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:134
                                   193       203       213       223       233       243       253       263       273       283       293       303       313    
          RNF41_HUMAN   184 NPNLQNLEETIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI 317
               SCOP domains ---------d2fzpa1 A:193-317 E3 ubiquitin-protein ligase NRDP1                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhheeeee.hhh.ee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh.eee.....eeeee.hhh...........eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7          -------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.8  PDB: A:201-317 UniProt: 201-317                                                                             Transcript 1 (2)
                 2fzp A 184 SSGLVPRGSTIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI 317
                                   193       203       213       223       233       243       253       263       273       283       293       303       313    

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNF41_HUMAN | Q9H4P4)
molecular function
    GO:0017160    Ral GTPase binding    Interacting selectively and non-covalently with Ral protein, any member of the Ral subfamily of the Ras superfamily of monomeric GTPases.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0005128    erythropoietin receptor binding    Interacting selectively and non-covalently with the erythropoietin receptor.
    GO:0005135    interleukin-3 receptor binding    Interacting selectively and non-covalently with the interleukin-3 receptor.
    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: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:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
    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:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0097191    extrinsic apoptotic signaling pathway    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0010498    proteasomal protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    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:0043408    regulation of MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
    GO:2000114    regulation of establishment of cell polarity    Any process that modulates the frequency, rate or extent of establishment of cell polarity.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045619    regulation of lymphocyte differentiation    Any process that modulates the frequency, rate or extent of lymphocyte differentiation.
    GO:0045637    regulation of myeloid cell differentiation    Any process that modulates the frequency, rate or extent of myeloid cell differentiation.
    GO:0051896    regulation of protein kinase B signaling    Any process that modulates the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:2000377    regulation of reactive oxygen species metabolic process    Any process that modulates the frequency, rate or extent of reactive oxygen species metabolic process.
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.

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        RNF41_HUMAN | Q9H4P42gwf

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