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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF MOUSE NRDP1
 
Authors :  S. Bouyain, D. J. Leahy
Date :  05 Jan 07  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  E3 Ubiquitin Ligase, Receptor-Binding Region, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Bouyain, D. J. Leahy
Structure-Based Mutagenesis Of The Substrate-Recognition Domain Of Nrdp1/Flrf Identifies The Binding Site For The Receptor Tyrosine Kinase Erbb3.
Protein Sci. V. 16 654 2007
PubMed-ID: 17384230  |  Reference-DOI: 10.1110/PS.062700307

(-) Compounds

Molecule 1 - RING FINGER PROTEIN 41
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET41
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNRDP1 C-TERMINAL DOMAIN
    GeneRNF41
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SCN-1Ligand/IonTHIOCYANATE ION
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SCN-1Ligand/IonTHIOCYANATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:114 , HOH A:122 , PRO A:304 , HIS A:312BINDING SITE FOR RESIDUE SCN A 318
2AC2SOFTWAREHOH A:102 , ARG A:231 , HIS A:295 , ASP B:222 , VAL B:224BINDING SITE FOR RESIDUE GOL A 319
3AC3SOFTWAREGLN A:284 , GLU A:303 , HIS A:312 , GLY A:313 , VAL A:314 , GLU A:315BINDING SITE FOR RESIDUE GOL A 320

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:303 -Pro A:304
2Glu B:303 -Pro B:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000963861ENSMUSE00000373913chr10:127848672-127848881210RNF41_MOUSE-00--
1.2ENSMUST000000963862ENSMUSE00000269383chr10:127852175-127852357183RNF41_MOUSE-00--
1.3ENSMUST000000963863ENSMUSE00000150269chr10:127865647-127865759113RNF41_MOUSE1-30300--
1.4ENSMUST000000963864ENSMUSE00000150279chr10:127872369-127872640272RNF41_MOUSE31-121910--
1.5ENSMUST000000963865ENSMUSE00000269351chr10:127873524-127873659136RNF41_MOUSE121-166460--
1.6ENSMUST000000963866ENSMUSE00000150267chr10:127874364-127874467104RNF41_MOUSE167-201352A:195-201
B:0-201
7
10
1.7bENSMUST000000963867bENSMUSE00000623329chr10:127875139-1278784943356RNF41_MOUSE201-3171172A:201-317
B:201-316
117
116

(-) 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:123
 aligned with RNF41_MOUSE | Q8BH75 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:123
                                   204       214       224       234       244       254       264       274       284       294       304       314   
          RNF41_MOUSE   195 EYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI 317
               SCOP domains d2ogba_ A: E3 ubiquitin-protein ligase NRDP1                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eee.hhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....ee.....eeeee.hhh...........eeeee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.6    -------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.7b  PDB: A:201-317 UniProt: 201-317                                                                            Transcript 1 (2)
                 2ogb A 195 EYNEILEWVNSLQPARVTRWGGmISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQmNRRYYENYVAKRIPGKQAVVVmACENQHmGDDmVQEPGLVmIFAHGVEEI 317
                                   204       214  |    224       234       244       254       264  |    274       284    |  294 |   | 304   |   314   
                                                217-MSE                                           267-MSE               289-MSE  |   |     308-MSE     
                                                                                                                               296-MSE                 
                                                                                                                                   300-MSE             

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with RNF41_MOUSE | Q8BH75 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:125
                                   201       211       221       231       241       251       261       271       281       291       301       311     
          RNF41_MOUSE   192 ETIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEE 316
               SCOP domains d2ogbb_ B: E3 ubiquitin-protein ligase NRDP1                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -USP8_interact-2ogbB01 B:193-315                                                                                            - Pfam domains (1)
           Pfam domains (2) -USP8_interact-2ogbB02 B:193-315                                                                                            - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh...ee.hhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh..ee.....eeeee.hhh...hhhhh...eeeee....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  ------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.7b  PDB: B:201-316 UniProt: 201-317 [INCOMPLETE]                                                              Transcript 1 (2)
                 2ogb B   0 STIEYNEILEWVNSLQPARVTRWGGmISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQmNRRYYENYVAKRIPGKQAVVVmACENQHmGDDmVQEPGLVmIFAHGVEE 316
                            ||     201       211     | 221       231       241       251       261     | 271       281       291    |  301      |311     
                            0|                     217-MSE                                           267-MSE               289-MSE  |   |     308-MSE    
                           193                                                                                                    296-MSE                
                                                                                                                                      300-MSE            

   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  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RNF41_MOUSE | Q8BH75)
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: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:1901525    negative regulation of macromitophagy    Any process that stops, prevents or reduces the frequency, rate or extent of macromitophagy.
    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: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.

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