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(-) Description

Title :  CRYSTAL STRUCTURE OF MDC1 FHA DOMAIN IN COMPLEX WITH A PHOSPHORYLATED PEPTIDE FROM THE MDC1 N-TERMINUS
 
Authors :  J. A. Clapperton, J. Lloyd, L. F. Haire, J. Li, S. J. Smerdon
Date :  17 Nov 11  (Deposition) - 28 Dec 11  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Fha Domain, Dna-Damage, Mdc1 Dimerization, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Jungmichel, J. A. Clapperton, J. Lloyd, F. J. Hari, C. Spycher, L. Pavic, J. Li, L. F. Haire, M. Bonalli, D. H. Larsen, C. Lukas, J. Lukas D. Macmillan, M. L. Nielsen, M. Stucki, S. J. Smerdon
The Molecular Basis Of Atm-Dependent Dimerization Of The Mdc1 Dna Damage Checkpoint Mediator.
Nucleic Acids Res. V. 40 3913 2012
PubMed-ID: 22234878  |  Reference-DOI: 10.1093/NAR/GKR1300

(-) Compounds

Molecule 1 - MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentN-TERMINAL FHA DOMAIN (RESIDUES 19-138)
    GeneMDC1, KIAA0170, NFBD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR FACTOR WITH BRCT DOMAINS 1
 
Molecule 2 - MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1
    ChainsD, E
    EngineeredYES
    FragmentPHOSPHORYLATED N-TERMINUS (RESIDUES 1-10)
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR FACTOR WITH BRCT DOMAINS 1
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABDE
Biological Unit 1 (1x)A D 
Biological Unit 2 (1x) B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (0, 0)

(no "Site" information available for 3UOT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:102 -Pro A:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.MDC1_HUMAN54-100
 
  2A:54-100
B:54-100
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.MDC1_HUMAN54-100
 
  1A:54-100
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.MDC1_HUMAN54-100
 
  1-
B:54-100

(-) Exons   (2, 6)

Asymmetric Unit (2, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.37aENST0000037640637aENSE00001835419chr6:30685666-30685022645MDC1_HUMAN-00--
1.40ENST0000037640640ENSE00001707939chr6:30682955-30682817139MDC1_HUMAN1-46464A:19-46
B:28-46
D:2-9
E:2-9
28
19
8
8
1.41iENST0000037640641iENSE00002149164chr6:30681960-30681580381MDC1_HUMAN46-1731282A:46-135
B:46-134
-
-
90
89
-
-
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_HUMAN1855-1894400--
1.47auENST0000037640647auENSE00001713998chr6:30671063-30670881183MDC1_HUMAN1895-1955610--
1.47bgENST0000037640647bgENSE00001800762chr6:30670654-30670529126MDC1_HUMAN1956-1997420--
1.47biENST0000037640647biENSE00001704145chr6:30670440-30670330111MDC1_HUMAN1998-2034370--
1.51dENST0000037640651dENSE00001891428chr6:30668409-30667584826MDC1_HUMAN2035-2089550--

(-) 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:117
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:117
                                    28        38        48        58        68        78        88        98       108       118       128       
           MDC1_HUMAN    19 QSSESLRCNVEPVGRLHIFSGAHGPEKDFPLHLGKNVVGRMPDCSVALPFPSISKQHAEIEILAWDKAPILRDCGSLNGTQILRPPKVLSPGVSHRLRDQELILFADLLCQYHRLDV 135
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh......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 1 (1) Exon 1.40  PDB: A:19-46     ----------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.41i  PDB: A:46-135 UniProt: 46-173 [INCOMPLETE]                                     Transcript 1 (2)
                 3uot A  19 QSSESLRCNVEPVGRLHIFSGAHGPEKDFPLHLGKNVVGRmPDCSVALPFPSISKQHAEIEILAWDKAPILRDCGSLNGTQILRPPKVLSPGVSHRLRDQELILFADLLCQYHRLDV 135
                                    28        38        48        58|       68        78        88        98       108       118       128       
                                                                   59-MSE                                                                        

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:107
                                    37        47        57        67        77        87        97       107       117       127       
           MDC1_HUMAN    28 VEPVGRLHIFSGAHGPEKDFPLHLGKNVVGRMPDCSVALPFPSISKQHAEIEILAWDKAPILRDCGSLNGTQILRPPKVLSPGVSHRLRDQELILFADLLCQYHRLD 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 1 (1) Exon 1.40          ---------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.41i  PDB: B:46-134 UniProt: 46-173 [INCOMPLETE]                                    Transcript 1 (2)
                 3uot B  28 VEPVGRLHIFSGAHGPEKDFPLHLGKNVVGRmPDCSVALPFPSISKQHAEIEILAWDKAPILRDCGSLNGTQILRPPKVLSPGVSHRLRDQELILFADLLCQYHRLD 134
                                    37        47        57 |      67        77        87        97       107       117       127       
                                                          59-MSE                                                                       

Chain D from PDB  Type:PROTEIN  Length:8
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:8
           MDC1_HUMAN     2 EDTQAIDW   9
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
           Transcript 1 (1) 1.40     Transcript 1 (1)
           Transcript 1 (2) -------- Transcript 1 (2)
                 3uot D   2 EDtQmIDW   9
                              | |   
                              4-TPO 
                                6-MSE

Chain E from PDB  Type:PROTEIN  Length:8
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:8
           MDC1_HUMAN     2 EDTQAIDW   9
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
           Transcript 1 (1) 1.40     Transcript 1 (1)
           Transcript 1 (2) -------- Transcript 1 (2)
                 3uot E   2 EDtQmIDW   9
                              | |   
                              4-TPO 
                                6-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  (0, 0)

(no "SCOP Domain" information available for 3UOT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (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 | Q146762ado 2azm 2etx 3k05 3ueo 3umz 3un0 3unm 3unn

(-) Related Entries Specified in the PDB File

3un0 CRYSTAL STRUCTURE OF MDC1 FHA DOMAIN