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(-) Description

Title :  MOUSE NP95 SRA DOMAIN NON-SPECIFIC DNA COMPLEX
 
Authors :  H. Hashimoto, J. R. Horton, X. Cheng
Date :  05 May 08  (Deposition) - 09 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym. Unit :  B,D,E
Biol. Unit 1:  B (1x),D (1x),E (1x)
Biol. Unit 2:  D,E  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  B,D,E  (2x)
Keywords :  Base Flipping, Cell Cycle, Developmental Protein, Dna Damage, Dna Repair, Dna-Binding, Ligase, Metal-Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Ubl Conjugation, Ubl Conjugation Pathway, Zinc, Zinc-Finger, Ligase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Hashimoto, J. R. Horton, X. Zhang, M. Bostick, S. E. Jacobsen, X. Cheng
The Sra Domain Of Uhrf1 Flips 5-Methylcytosine Out Of The Dna Helix
Nature V. 455 826 2008
PubMed-ID: 18772888  |  Reference-DOI: 10.1038/NATURE07280
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UHRF1
    ChainsB
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPXC666
    Expression System StrainBL21(DE3)-GOLD CELLS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSRA DOMAIN, RESIDUES 419-628
    GeneNP95
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymUBIQUITIN-LIKE PHD AND RING FINGER DOMAIN- CONTAINING PROTEIN 1, UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN 1, NUCLEAR ZINC FINGER PROTEIN NP95, NUCLEAR PROTEIN 95
 
Molecule 2 - DNA (5'- D(*DAP*DAP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DTP*DT)-3')
    ChainsD, E
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit BDE
Biological Unit 1 (1x)B (1x)D (1x)E (1x)
Biological Unit 2 (1x) DE
Biological Unit 3 (1x)B  
Biological Unit 4 (2x)BDE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:449 , HIS B:450 , VAL B:451 , ALA B:452 , DT D:12BINDING SITE FOR RESIDUE PO4 B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZO2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZO2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZO2)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YDGPS51015 YDG domain profile.UHRF1_MOUSE424-586  1B:424-586
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YDGPS51015 YDG domain profile.UHRF1_MOUSE424-586  1B:424-586
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YDGPS51015 YDG domain profile.UHRF1_MOUSE424-586  0-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YDGPS51015 YDG domain profile.UHRF1_MOUSE424-586  1B:424-586
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YDGPS51015 YDG domain profile.UHRF1_MOUSE424-586  2B:424-586

(-) Exons   (0, 0)

(no "Exon" information available for 2ZO2)

(-) 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 B from PDB  Type:PROTEIN  Length:201
 aligned with UHRF1_MOUSE | Q8VDF2 from UniProtKB/Swiss-Prot  Length:782

    Alignment length:209
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616         
          UHRF1_MOUSE   417 IVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTRQLGLTMQYPEGYLEALANKEKS 625
               SCOP domains d2zo2b_ B: E3 ubiquitin-protein ligase UHRF1                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---YDG_SRA-2zo2B01 B:420-590                                                                                                                                                  ----------------------------------- Pfam domains
         Sec.struct. author .................ee.hhhhhhhh.........eeee...eeeeeee............eeeee......--------.........hhhhhhhhhh........ee..hhhhh.eeeeeee.hhh..........eeeeeeeeeeeeeeee.....eeeeeeeee........hhhhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------YDG  PDB: B:424-586 UniProt: 424-586                                                                                                                               --------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zo2 B 417 HMPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNYFTYTGSGGRD--------GQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTRQLGLTMQYPEGYLEALANKEKS 625
                                   426       436       446       456       466       476       486   |     -  |    506       516       526       536       546       556       566       576       586       596       606       616         
                                                                                                   490      499                                                                                                                              

Chain D from PDB  Type:DNA  Length:12
                                            
                 2zo2 D   1 AACTGCGCAGTT  12
                                    10  

Chain E from PDB  Type:DNA  Length:12
                                            
                 2zo2 E  13 AACTGCGCAGTT  24
                                    22  

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZO2)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)
Chain B   (UHRF1_MOUSE | Q8VDF2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0044729    hemi-methylated DNA-binding    Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0008327    methyl-CpG binding    Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0031493    nucleosomal histone binding    Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
    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:0032776    DNA methylation on cytosine    The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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:0010390    histone monoubiquitination    The modification of histones by addition of a single ubiquitin group.
    GO:0016574    histone ubiquitination    The modification of histones by addition of ubiquitin groups.
    GO:0010216    maintenance of DNA methylation    Any process involved in maintaining the methylation state of a nucleotide sequence.
    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:0032270    positive regulation of cellular protein metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
    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: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:0090308    regulation of methylation-dependent chromatin silencing    Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043434    response to peptide hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0000791    euchromatin    A dispersed and relatively uncompacted form of chromatin.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005657    replication fork    The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UHRF1_MOUSE | Q8VDF22zkd 2zke 2zkf 2zkg 2zo0 2zo1 3f8i 3f8j 3fde

(-) Related Entries Specified in the PDB File

2zo0 SRA-DNA SPECIFIC COMPLEX 1
2zo1 SRA-DNA SPECIFIC COMPLEX 2