Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE CRB2-BRCT2 DOMAIN
 
Authors :  M. L. Kilkenny, S. M. Roe, L. H. Pearl
Date :  03 Jul 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Brct, Nucleus, Cell Cycle, Dna Damage, Dna Replication Inhibitor, Phosphoprotein, Checkpoint Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. L. Kilkenny, A. Dore, S. M. Roe, K. Nestoras, J. C. Y. Ho, F. Z. Watts, L. H. Pearl
Structural And Functional Analysis Of The Crb2- Brct2 Domain Reveals Distinct Roles In Checkpoint Signaling And Dna Damage Repair.
Genes Dev. V. 22 2034 2008
PubMed-ID: 18676809  |  Reference-DOI: 10.1101/GAD.472808

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RHP9
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainPRSETB
    Expression System Taxid562
    FragmentBRCT DOMAIN, RESIDUE 538-778
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    StrainSP.011
    SynonymRAD9 HOMOLOG, CHECKPOINT PROTEIN CRB2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PR3Ligand/IonPRASEODYMIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , ASP A:22 , HOH A:2002 , HOH A:2003BINDING SITE FOR RESIDUE PR A1259
2AC2SOFTWAREGLU A:33 , ASP B:21 , ASP B:22BINDING SITE FOR RESIDUE PR A1260
3AC3SOFTWAREGLU A:33 , ASP A:34 , ASP B:22 , SER B:83 , HOH B:2002 , HOH B:2003BINDING SITE FOR RESIDUE PR A1261

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:222 -A:238
2B:222 -B:238

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:29 -Pro A:30
2Val A:217 -Ala A:218
3His A:219 -Leu A:220
4Gly B:29 -Pro B:30
5Cys B:238 -Pro B:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VXB)

(-) 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:225
 aligned with RHP9_SCHPO | P87074 from UniProtKB/Swiss-Prot  Length:778

    Alignment length:241
                                   547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777 
           RHP9_SCHPO   538 LIFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFKSKQKKLRHLKPQKRSKSWNQAFVVSDTFSRKVKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSPYLLASGYSHRLDCTLSQRIEPFDTTDSLYDRLLARKGPLFGKKILFIIPEAKSWQKKIENTEQGQKALAHVYHALALGADVEIRPNVAHLECDLILTMDGNIVDETNCPVVDPEWIVECLISQSDIST 778
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.........hhhhhhhhhhhh..ee....hhhh......----.......hhhhhhh.eeeee......hhhhhhhhhhh..ee.hhhhhhhhhhh....hhhh..eeeee....eeee..........hhhhhhhhh.......eeee...------------.hhhhhhhhhhhhhhh..eee...........eee.............eehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxb A  18 LIFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFK----KLRHLKPQKRSKSWNQAFVVSDTFSRKVKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSPYLLASGYSHRLDCTLSQRIEPFDTTDSLYDRLLARKGPLFGKKILFIIP------------EQGQKALAHVYHALALGADVEIRPNVAHLECDLILTMDGNIVDETNCPVVDPEWIVECLISQSDIST 258
                                    27        37        47        57        |-   |    77        87        97       107       117       127       137       147       157       167       177 |       -    |  197       207       217       227       237       247       257 
                                                                           66   71                                                                                                         179          192                                                                  

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with RHP9_SCHPO | P87074 from UniProtKB/Swiss-Prot  Length:778

    Alignment length:241
                                   547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777 
           RHP9_SCHPO   538 LIFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFKSKQKKLRHLKPQKRSKSWNQAFVVSDTFSRKVKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSPYLLASGYSHRLDCTLSQRIEPFDTTDSLYDRLLARKGPLFGKKILFIIPEAKSWQKKIENTEQGQKALAHVYHALALGADVEIRPNVAHLECDLILTMDGNIVDETNCPVVDPEWIVECLISQSDIST 778
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.........hhhhhhhhhhh...ee....hhhh..........ee.....hhhhhhh.eeeee......hhhhhhhhhhh..ee.hhhhhhhhhhh....hhhh..eeeee....eeee..........hhhhhhhhh.......eeeee..------------hhhhhhhhhhhhhhhh..eeeee.........eeee...-----....eehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxb B  18 LIFDDCVFAFSGPVHEDAYDRSALETVVQDHGGLVLDTGLRPLFNDPFKSKQKKLRHLKPQKRSKSWNQAFVVSDTFSRKVKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSPYLLASGYSHRLDCTLSQRIEPFDTTDSLYDRLLARKGPLFGKKILFIIP------------EQGQKALAHVYHALALGADVEIRPNVAHLECDLILTMDG-----TNCPVVDPEWIVECLISQSDIST 258
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177 |       -    |  197       207       217       227  |    237       247       257 
                                                                                                                                                                                           179          192                                   230   236                      

   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 2VXB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RHP9_SCHPO | P87074)
molecular function
    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: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).
biological process
    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: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:0033314    mitotic DNA replication checkpoint    A cell cycle checkpoint that acts during a mitotic cell cycle and prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.
    GO:0007095    mitotic G2 DNA damage checkpoint    A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage.
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:1902402    signal transduction involved in mitotic DNA damage checkpoint    Any intracellular signal transduction that is involved in mitotic DNA damage checkpoint.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0035861    site of double-strand break    A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys B:238 - Pro B:239   [ RasMol ]  
    Gly A:29 - Pro A:30   [ RasMol ]  
    Gly B:29 - Pro B:30   [ RasMol ]  
    His A:219 - Leu A:220   [ RasMol ]  
    Val A:217 - Ala A:218   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2vxb
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RHP9_SCHPO | P87074
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RHP9_SCHPO | P87074
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RHP9_SCHPO | P870742fhd 2vxc 4bu0 4bu1

(-) Related Entries Specified in the PDB File

2vxc STRUCTURE OF THE CRB2-BRCT2 DOMAIN COMPLEX WITH PHOSPHOPEPTIDE.