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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MAMMALIAN MDC1 FHA DOMAIN
 
Authors :  H. H. Wu, P. Y. Wu, K. F. Huang, Y. Y. Kao, M. D. Tsai
Date :  28 Dec 11  (Deposition) - 01 Feb 12  (Release) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Cycle, Fha Domain, Dna-Damage, Mdc1 Dimerization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Wu, P. Y. Wu, K. F. Huang, Y. Y. Kao, M. D. Tsai
Structural Delineation Of Mdc1-Fha Domain Binding With Chk2-Pthr68.
Biochemistry 2012
PubMed-ID: 22211259  |  Reference-DOI: 10.1021/BI201709W

(-) Compounds

Molecule 1 - MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FHA DOMAIN (UNP RESIDUES 29-139)
    Gene: MDC1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:58 , SER A:72 , LYS A:73BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREPRO A:103 , PRO A:104 , ARG A:105 , ARG B:58 , SER B:72 , LYS B:73 , GLN B:99BINDING SITE FOR RESIDUE SO4 B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VA1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:102 -Pro A:103
2Lys B:102 -Pro B:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VA1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.MDC1_MOUSE54-100
 		  2A:54-100
B:54-100

(-) Exons   (0, 0)

(no "Exon" information available for 3VA1)

(-) 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:107
 aligned with MDC1_MOUSE | Q5PSV9 from UniProtKB/Swiss-Prot  Length:1707

    Alignment length:107
                                    38        48        58        68        78        88        98       108       118       128       
           MDC1_MOUSE    29 EPIGQLRLFSGTHGPERDFPLYLGKNVVGRSPDCSVALPFPSISKQHAVIEISAWNKAPILQDCGSLNGTQIVKPPRVLPPGVSHRLRDQELILFADFPCQYHRLDV 135
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........eeeee..eeeeee......ee..........eeeee.......eeee......eee....ee......ee.....eeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FHA_DOMAIN  PDB: A:54-100 UniProt: 54-100      ----------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3va1 A  29 EPIGQLRLFSGTHGPERDFPLYLGKNVVGRSPDCSVALPFPSISKQHAVIEISAWNKAPILQDCGSLNGTQIVKPPRVLPPGVSHRLRDQELILFADFPCQYHRLDV 135
                                    38        48        58        68        78        88        98       108       118       128       


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with MDC1_MOUSE | Q5PSV9 from UniProtKB/Swiss-Prot  Length:1707

    Alignment length:107
                                    37        47        57        67        77        87        97       107       117       127       
           MDC1_MOUSE    28 VEPIGQLRLFSGTHGPERDFPLYLGKNVVGRSPDCSVALPFPSISKQHAVIEISAWNKAPILQDCGSLNGTQIVKPPRVLPPGVSHRLRDQELILFADFPCQYHRLD 134
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee........eeeee..eeeeee......ee..........eeeee.......eeee......eee....ee......ee.....eeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------FHA_DOMAIN  PDB: B:54-100 UniProt: 54-100      ---------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3va1 B  28 MEPIGQLRLFSGTHGPERDFPLYLGKNVVGRSPDCSVALPFPSISKQHAVIEISAWNKAPILQDCGSLNGTQIVKPPRVLPPGVSHRLRDQELILFADFPCQYHRLD 134
                                    37        47        57        67        77        87        97       107       117       127
   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 3VA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VA1)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MDC1_MOUSE | Q5PSV9)
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.
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.
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_MOUSE | Q5PSV9: 3va4

(-) Related Entries Specified in the PDB File

3va4