3K05 - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF MDC1 BRCT T2067D IN COMPLEX WITH A MINIMAL RECOGNITION TETRAPEPTIDE WITH AN AMIDATED C-TERMINUS

Authors :   S. J. Campbell, R. A. Edwards, J. N. Glover

Date :   24 Sep 09 (Deposition) - 02 Mar 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.33

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Brct Domain, Protein-Peptide Complex, Phospho Protein Binding, H2Ax, Dna Damage Response, Cell Cycle, Dna Damage, Dna Repair, Nucleus, Phosphoprotein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Campbell, R. A. Edwards, J. N. Glover
Comparison Of The Structures And Peptide Binding Specificities Of The Brct Domains Of Mdc1 And Brca1
Structure V. 18 167 2010
PubMed-ID: 20159462 | Reference-DOI: 10.1016/J.STR.2009.12.008

Molecule 1 - MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKM596
	Expression System Strain	:	BL21 GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BRCT DOMAIN (UNP RESIDUES 1892 TO 2089)
	Gene	:	KIAA0170, MDC1, NFBD1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEAR FACTOR WITH BRCT DOMAINS 1

Molecule 2 - PHOSPHO PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	Organism Taxid	:	9606
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS. THE PEPTIDE IS CHEMICALLY SYNTHESIZED.
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NH2	2	Mod. Amino Acid	AMINO GROUP
3	SEP	2	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NH2	1	Mod. Amino Acid	AMINO GROUP
3	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	NH2	1	Mod. Amino Acid	AMINO GROUP
3	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:2008 , GLU A:2063 , HOH B:69 , HOH B:186 , VAL B:1901 , ALA B:1903 , TYR C:142 , NH2 C:143	BINDING SITE FOR RESIDUE GOL B 1
2	AC2	SOFTWARE	HOH B:78 , HOH B:113 , HOH B:300 , HOH B:389 , ARG B:1943 , ARG B:1994 , SER B:2019 , GLY B:2022	BINDING SITE FOR RESIDUE GOL B 2090
3	AC3	SOFTWARE	HOH A:71 , ARG A:1943 , ARG A:1994 , SER A:2019 , CYS A:2020 , GLY A:2022 , HOH B:37 , HOH B:289 , PRO B:2047 , SER B:2050	BINDING SITE FOR RESIDUE GOL A 1
4	AC4	SOFTWARE	HOH B:82 , HOH B:84 , HOH B:235 , HOH B:409 , PHE B:1897 , GLY B:1899 , VAL B:1900 , LYS B:1936 , GLN C:140 , SEP D:139	BINDING SITE FOR RESIDUE GOL B 2091

(no "SS Bond" information available for 3K05)

Asymmetric Unit

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051170	R	1904	Q	MDC1_HUMAN	Polymorphism	28994876	A/B	R	1904	Q

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051170	R	1904	Q	MDC1_HUMAN	Polymorphism	28994876	A	R	1904	Q

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051170	R	1904	Q	MDC1_HUMAN	Polymorphism	28994876	B	R	1904	Q

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MDC1_HUMAN	1892-1970	2	A:1892-1970 B:1892-1970

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MDC1_HUMAN	1892-1970	1	A:1892-1970 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MDC1_HUMAN	1892-1970	1	- B:1892-1970

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.37a	ENST00000376406	37a	ENSE00001835419	chr6:30685666-30685022	645	MDC1_HUMAN	-	0	0	-	-
1.40	ENST00000376406	40	ENSE00001707939	chr6:30682955-30682817	139	MDC1_HUMAN	1-46	46	0	-	-
1.41i	ENST00000376406	41i	ENSE00002149164	chr6:30681960-30681580	381	MDC1_HUMAN	46-173	128	0	-	-
1.41j	ENST00000376406	41j	ENSE00001677117	chr6:30681494-30681425	70	MDC1_HUMAN	173-196	24	0	-	-
1.41n	ENST00000376406	41n	ENSE00001672479	chr6:30681131-30679651	1481	MDC1_HUMAN	196-690	495	0	-	-
1.41v	ENST00000376406	41v	ENSE00001732269	chr6:30679503-30679444	60	MDC1_HUMAN	690-710	21	0	-	-
1.42b	ENST00000376406	42b	ENSE00001773945	chr6:30679281-30679189	93	MDC1_HUMAN	710-741	32	0	-	-
1.45j	ENST00000376406	45j	ENSE00001790042	chr6:30676134-30675343	792	MDC1_HUMAN	741-1005	265	0	-	-
1.45q	ENST00000376406	45q	ENSE00001682597	chr6:30675231-30675161	71	MDC1_HUMAN	1005-1028	24	0	-	-
1.47d	ENST00000376406	47d	ENSE00001757825	chr6:30673875-30671398	2478	MDC1_HUMAN	1029-1854	826	0	-	-
1.47aq	ENST00000376406	47aq	ENSE00001680569	chr6:30671314-30671195	120	MDC1_HUMAN	1855-1894	40	2	A:1891-1894 B:1890-1894	4 5
1.47au	ENST00000376406	47au	ENSE00001713998	chr6:30671063-30670881	183	MDC1_HUMAN	1895-1955	61	2	A:1895-1955 B:1895-1955	61 61
1.47bg	ENST00000376406	47bg	ENSE00001800762	chr6:30670654-30670529	126	MDC1_HUMAN	1956-1997	42	2	A:1956-1997 B:1956-1997	42 42
1.47bi	ENST00000376406	47bi	ENSE00001704145	chr6:30670440-30670330	111	MDC1_HUMAN	1998-2034	37	2	A:1998-2034 B:1998-2034	37 37
1.51d	ENST00000376406	51d	ENSE00001891428	chr6:30668409-30667584	826	MDC1_HUMAN	2035-2089	55	2	A:2035-2083 B:2035-2089	49 55

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:193
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:193
                                  1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040      2050      2060      2070      2080   
          MDC1_HUMAN   1891 TAPKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEAKPEAFVLSP 2083
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhh..ee..hhhhh.eee......hhhhhhhhhhh..eehhhhhhhhhhhh....hhhhh..hhhhhhhhh.hhhhhhhhhhhh......eeee......hhhhhhhhhhhh..eee..........eeee.hhhhhhhhhhhhhhh..ee.hhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -BRCT  PDB: A:1892-1970 UniProt: 1892-1970                                      ----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 1.47Exon 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:2035-2083 UniProt: 2035-2089   Transcript 1
                3k05 A 1891 TAPKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLDGVLKQEAKPEAFVLSP 2083
                                  1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040      2050      2060      2070      2080

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with MDC1_HUMAN | Q14676 from UniProtKB/Swiss-Prot  Length:2089

    Alignment length:200
                                  1899      1909      1919      1929      1939      1949      1959      1969      1979      1989      1999      2009      2019      2029      2039      2049      2059      2069      2079      2089
          MDC1_HUMAN   1890 STAPKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTGVLKQEAKPEAFVLSPLEMSST 2089
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhh..ee..hhhhh.eeee.....hhhhhhhhhhh..eeehhhhhhhhhhh....hhhhh..hhhhhhhhh.hhhhhhhhhhhh......eeee......hhhhhhhhhhhh..eee..........eeee.hhhhhhhhhhhhhhh..ee.hhhhhhhhhhh..hhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --BRCT  PDB: B:1892-1970 UniProt: 1892-1970                                      ----------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 1.47aExon 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:2035-2089 UniProt: 2035-2089         Transcript 1
                3k05 B 1890 GTAPKVLFTGVVDARGERAVLALGGSLAGSAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSRKAGFFLPPDEYVVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEIISCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLDGVLKQEAKPEAFVLSPLEMSST 2089
                                  1899      1909      1919      1929      1939      1949      1959      1969      1979      1989      1999      2009      2019      2029      2039      2049      2059      2069      2079      2089

Chain C from PDB  Type:PROTEIN  Length:5
                                      
               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 ----- Transcript
                3k05 C  139 sQEYx  143
                            |   |
                          139-SEP
                              143-NH2

Chain D from PDB  Type:PROTEIN  Length:5
                                      
               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 ----- Transcript
                3k05 D  139 sQEYx  143
                            |   |
                            |   |
                          139-SEP
                              143-NH2

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 '\|'

(no "SCOP Domain" information available for 3K05)

(no "CATH Domain" information available for 3K05)

(no "Pfam Domain" information available for 3K05)

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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	MDC1_HUMAN \| Q14676	:	2ado 2azm 2etx 3ueo 3umz 3un0 3unm 3unn 3uot

Description

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Ligands, Modified Residues, Ions (3, 8)

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