2IG0 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF 53BP1/METHYLATED HISTONE PEPTIDE COMPLEX

Authors :   G. Mer

Date :   22 Sep 06 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tandem Tudor Domains, Dimethylated Histone H4, Dna Repair, Cell Cycle Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. V. Botuyan, J. Lee, I. M. Ward, J. E. Kim, J. R. Thompson, J. Chen, G. Mer
Structural Basis For The Methylation State-Specific Recognition Of Histone H4-K20 By 53Bp1 And Crb2 In Dna Repair.
Cell(Cambridge, Mass. ) V. 127 1361 2006
PubMed-ID: 17190600 | Reference-DOI: 10.1016/J.CELL.2006.10.043
(for further references see the PDB file header)

Molecule 1 - TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PTEV
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
	Gene	:	TP53BP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	P53-BINDING PROTEIN 1, P53BP1, 53BP1

Molecule 2 - DIMETHYLATED HISTONE H4-K20 PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:149 , LYS A:1559 , LYS A:1563 , GLU A:1564 , SER A:1565 , GLU A:1573 , ARG A:1578	BINDING SITE FOR RESIDUE SO4 A 201

(no "SS Bond" information available for 2IG0)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:1536	-	Pro A:1537

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_038689	G	1488	W	TP53B_HUMAN	Polymorphism	11554564	A	G	1488	W

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

(no "PROSITE Motif" information available for 2IG0)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000263801	1b	ENSE00001344404	chr15:43802812-43802568	245	TP53B_HUMAN	-	0	0	-	-
1.4	ENST00000263801	4	ENSE00001713374	chr15:43784666-43784482	185	TP53B_HUMAN	1-59	59	0	-	-
1.5	ENST00000263801	5	ENSE00001046179	chr15:43784293-43784200	94	TP53B_HUMAN	60-91	32	0	-	-
1.6	ENST00000263801	6	ENSE00001046160	chr15:43783951-43783867	85	TP53B_HUMAN	91-119	29	0	-	-
1.7	ENST00000263801	7	ENSE00001046169	chr15:43773220-43773093	128	TP53B_HUMAN	119-162	44	0	-	-
1.8	ENST00000263801	8	ENSE00001046152	chr15:43772215-43772057	159	TP53B_HUMAN	162-215	54	0	-	-
1.9	ENST00000263801	9	ENSE00001046208	chr15:43771724-43771595	130	TP53B_HUMAN	215-258	44	0	-	-
1.10	ENST00000263801	10	ENSE00001046166	chr15:43769957-43769791	167	TP53B_HUMAN	258-314	57	0	-	-
1.11	ENST00000263801	11	ENSE00001046193	chr15:43767892-43767763	130	TP53B_HUMAN	314-357	44	0	-	-
1.12	ENST00000263801	12	ENSE00001046180	chr15:43766965-43766871	95	TP53B_HUMAN	357-389	33	0	-	-
1.13	ENST00000263801	13	ENSE00001046161	chr15:43762264-43762056	209	TP53B_HUMAN	389-458	70	0	-	-
1.14a	ENST00000263801	14a	ENSE00001046204	chr15:43749416-43748090	1327	TP53B_HUMAN	459-901	443	0	-	-
1.15a	ENST00000263801	15a	ENSE00001046164	chr15:43739683-43739564	120	TP53B_HUMAN	901-941	41	0	-	-
1.17	ENST00000263801	17	ENSE00001628086	chr15:43738788-43738585	204	TP53B_HUMAN	941-1009	69	0	-	-
1.18a	ENST00000263801	18a	ENSE00001675565	chr15:43733781-43733724	58	TP53B_HUMAN	1009-1028	20	0	-	-
1.19a	ENST00000263801	19a	ENSE00001595850	chr15:43730614-43730522	93	TP53B_HUMAN	1028-1059	32	0	-	-
1.20b	ENST00000263801	20b	ENSE00001729133	chr15:43724875-43724392	484	TP53B_HUMAN	1059-1220	162	0	-	-
1.21a	ENST00000263801	21a	ENSE00001648704	chr15:43720366-43720214	153	TP53B_HUMAN	1221-1271	51	0	-	-
1.22a	ENST00000263801	22a	ENSE00001612038	chr15:43714324-43714053	272	TP53B_HUMAN	1272-1362	91	0	-	-
1.23b	ENST00000263801	23b	ENSE00001657667	chr15:43713372-43713223	150	TP53B_HUMAN	1362-1412	51	0	-	-
1.24a	ENST00000263801	24a	ENSE00001735071	chr15:43712933-43712503	431	TP53B_HUMAN	1412-1556	145	1	A:1485-1556	72
1.25b	ENST00000263801	25b	ENSE00001666968	chr15:43708614-43708423	192	TP53B_HUMAN	1556-1620	65	1	A:1556-1603	48
1.26	ENST00000263801	26	ENSE00001684657	chr15:43708007-43707792	216	TP53B_HUMAN	1620-1692	73	0	-	-
1.28b	ENST00000263801	28b	ENSE00001734669	chr15:43705532-43705317	216	TP53B_HUMAN	1692-1764	73	0	-	-
1.30	ENST00000263801	30	ENSE00001771292	chr15:43701939-43701845	95	TP53B_HUMAN	1764-1795	32	0	-	-
1.31b	ENST00000263801	31b	ENSE00001727562	chr15:43701294-43701095	200	TP53B_HUMAN	1796-1862	67	0	-	-
1.32	ENST00000263801	32	ENSE00001751396	chr15:43700286-43700141	146	TP53B_HUMAN	1862-1911	50	0	-	-
1.33b	ENST00000263801	33b	ENSE00001841464	chr15:43699768-43699407	362	TP53B_HUMAN	1911-1972	62	0	-	-

2.1	ENST00000377803	1	ENSE00001475159	chr6:26104104-26104518	415	H4_HUMAN	1-127	127	1	B:19-20	2

Asymmetric/Biological Unit

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Chain A from PDB  Type:PROTEIN  Length:119
 aligned with TP53B_HUMAN | Q12888 from UniProtKB/Swiss-Prot  Length:1972

    Alignment length:119
                                  1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594         
         TP53B_HUMAN   1485 SFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG 1603
               SCOP domains d2ig0a1 A:1485-1537 p53-binding protein 1, 53BP1     d2ig0a2 A:1538-1603 p53-binding protein 1, 53BP1                   SCOP domains
               CATH domains 2ig0A01 A:1485-1538                                   2ig0A02 A:1539-1603  [code=2.30.30.30, no name defined]           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......eeeeeeeeeee..eeeeee....eeeee...ee.........eeeee.....eeeeeeeeeeee..eeeeeeee..eeeeee...ee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---W------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.24a  PDB: A:1485-1556 UniProt: 1412-1556 [INCOMPLETE]            ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.25b  PDB: A:1556-1603 UniProt: 1556-1620  Transcript 1 (2)
                2ig0 A 1485 SFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG 1603
                                  1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594

Chain B from PDB  Type:PROTEIN  Length:2
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:2
            H4_HUMAN     79 RK   80
               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 2 2. Transcript 2
                2ig0 B   19 Rk   20
                             |
                             |
                            20-MLY

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: Tudor domain (24)

Protein domain: p53-binding protein 1, 53BP1 (5)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d2ig0a1	A:1485-1537
1b	d2ig0a2	A:1538-1603

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.140, no name defined] (12)

Human (Homo sapiens) (10)

2ig0A01

A:1485-1538

Homologous Superfamily: [code=2.30.30.30, no name defined] (111)

Human (Homo sapiens) (10)

2ig0A02

A:1539-1603

(no "Pfam Domain" information available for 2IG0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TP53B_HUMAN | Q12888)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	GO:0001104	RNA polymerase II transcription cofactor activity	Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of 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:0000077	DNA damage checkpoint	A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
	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: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:0071481	cellular response to X-ray	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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
	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:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	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.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000777	condensed chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	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.

Chain B (H4_HUMAN | P62805)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0034080	CENP-A containing nucleosome assembly	The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
	GO:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:1904837	beta-catenin-TCF complex assembly	The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	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:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	GO:0045653	negative regulation of megakaryocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0051290	protein heterotetramerization	The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
	GO:0016233	telomere capping	A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
	GO:0032200	telomere organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TP53B_HUMAN \| Q12888
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2IG0)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (3, 3)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (50, 56)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File