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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BRCT REPEAT REGION FROM THE MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1, MDC1
 
Authors :  M. S. Lee, R. A. Edwards, G. L. Thede, J. N. Glover
Date :  20 Jul 05  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Brct Repeats, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Lee, R. A. Edwards, G. L. Thede, J. N. Glover
Structure Of The Brct Repeat Domain Of Mdc1 And Its Specificity For The Free Cooh-Terminal End Of The {Gamma}-H2Ax Histone Tail.
J. Biol. Chem. V. 280 32053 2005
PubMed-ID: 16049003  |  Reference-DOI: 10.1074/JBC.C500273200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainGOLD99
    Expression System Taxid562
    Expression System VectorPDEST15
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1891-2086
    GeneMDC1, KIAA0170, NFBD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR FACTOR WITH BRCT DOMAINS 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2ADO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:2008 -Pro A:2009
2Gln B:2008 -Pro B:2009

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051170R1904QMDC1_HUMANPolymorphism28994876A/BR1904Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051170R1904QMDC1_HUMANPolymorphism28994876AR1904Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051170R1904QMDC1_HUMANPolymorphism28994876BR1904Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.MDC1_HUMAN1892-1970
 
  2A:1892-1970
B:1892-1970
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.MDC1_HUMAN1892-1970
 
  1A:1892-1970
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.MDC1_HUMAN1892-1970
 
  1-
B:1892-1970

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.37aENST0000037640637aENSE00001835419chr6:30685666-30685022645MDC1_HUMAN-00--
1.40ENST0000037640640ENSE00001707939chr6:30682955-30682817139MDC1_HUMAN1-46460--
1.41iENST0000037640641iENSE00002149164chr6:30681960-30681580381MDC1_HUMAN46-1731280--
1.41jENST0000037640641jENSE00001677117chr6:30681494-3068142570MDC1_HUMAN173-196240--
1.41nENST0000037640641nENSE00001672479chr6:30681131-306796511481MDC1_HUMAN196-6904950--
1.41vENST0000037640641vENSE00001732269chr6:30679503-3067944460MDC1_HUMAN690-710210--
1.42bENST0000037640642bENSE00001773945chr6:30679281-3067918993MDC1_HUMAN710-741320--
1.45jENST0000037640645jENSE00001790042chr6:30676134-30675343792MDC1_HUMAN741-10052650--
1.45qENST0000037640645qENSE00001682597chr6:30675231-3067516171MDC1_HUMAN1005-1028240--
1.47dENST0000037640647dENSE00001757825chr6:30673875-306713982478MDC1_HUMAN1029-18548260--
1.47aqENST0000037640647aqENSE00001680569chr6:30671314-30671195120MDC1_HUMAN1855-1894402A:1892-1894
B:1891-1894
3
4
1.47auENST0000037640647auENSE00001713998chr6:30671063-30670881183MDC1_HUMAN1895-1955612A:1895-1955
B:1895-1955
61
61
1.47bgENST0000037640647bgENSE00001800762chr6:30670654-30670529126MDC1_HUMAN1956-1997422A:1956-1997
B:1956-1997
42
42
1.47biENST0000037640647biENSE00001704145chr6:30670440-30670330111MDC1_HUMAN1998-2034372A:1998-2034
B:1998-2034
37
37
1.51dENST0000037640651dENSE00001891428chr6:30668409-30667584826MDC1_HUMAN2035-2089552A:2035-2085
B:2035-2085
51
51

(-) 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:194
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:194
                                  1901      1911      1921      1931      1941      1951      1961      1971      1981      1991      2001      2011      2021      2031      2041      2051      2061      2071      2081    
          MDC1_HUMAN   1892 APKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEAKPEAFVLSPLE 2085
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhh..ee........eee......hhhhhhhhhhh..ee.hhhhhhhhhhh....hhhhh..hhhhhhhhh.hhhhhhhhhhhh......eeee......hhhhhhhhhhhh..ee...........eeee.hhhhhhhhhhhhhhh..eehhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BRCT  PDB: A:1892-1970 UniProt: 1892-1970                                      ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 1.4Exon 1.47au  PDB: A:1895-1955 UniProt: 1895-1955             Exon 1.47bg  PDB: A:1956-1997             Exon 1.47bi  PDB: A:1998-2034        Exon 1.51d  PDB: A:2035-2085 UniProt: 2035-2089     Transcript 1
                2ado A 1892 APKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEAKPEAFVLSPLE 2085
                                  1901      1911      1921      1931      1941      1951      1961      1971      1981      1991      2001      2011      2021      2031      2041      2051      2061      2071      2081    

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:195
                                  1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040      2050      2060      2070      2080     
          MDC1_HUMAN   1891 TAPKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEAKPEAFVLSPLE 2085
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhh..ee........eee......hhhhhhhhhhh..ee.hhhhhhhhhhh....hhhhh..hhhhhhhhh.hhhhhhhhhhhh......eeee......hhhhhhhhhhhh..ee...........eeee.hhhhhhhhhhhhhhh..eehhhhhhhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -BRCT  PDB: B:1892-1970 UniProt: 1892-1970                                      ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 1.47Exon 1.47au  PDB: B:1895-1955 UniProt: 1895-1955             Exon 1.47bg  PDB: B:1956-1997             Exon 1.47bi  PDB: B:1998-2034        Exon 1.51d  PDB: B:2035-2085 UniProt: 2035-2089     Transcript 1
                2ado B 1891 TAPKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEAKPEAFVLSPLE 2085
                                  1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040      2050      2060      2070      2080     

   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 2ADO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MDC1_HUMAN | Q14676)
molecular function
    GO:0070975    FHA domain binding    Interacting selectively and non-covalently with a FHA domain of a protein. The FHA domain is a phosphopeptide recognition domain found in many regulatory proteins, and consists of approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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: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: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:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0031573    intra-S DNA damage checkpoint    A mitotic cell cycle checkpoint that slows DNA synthesis in response to DNA damage by the prevention of new origin firing and the stabilization of slow replication fork progression.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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
        MDC1_HUMAN | Q146762azm 2etx 3k05 3ueo 3umz 3un0 3unm 3unn 3uot

(-) Related Entries Specified in the PDB File

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