3T6R - JenaLib

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Title :   STRUCTURE OF UHRF1 IN COMPLEX WITH UNMODIFIED H3 N-TERMINAL TAIL

Authors :   S. Xie, J. Jakoncic, C. M. Qian

Date :   29 Jul 11 (Deposition) - 23 Nov 11 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Zinc Finger, Histone Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Xie, J. Jakoncic, C. M. Qian
Uhrf1 Double Tudor Domain And The Adjacent Phd Finger Act Together To Recognize K9Me3-Containing Histone H3 Tail
J. Mol. Biol. V. 415 318 2012
PubMed-ID: 22100450 | Reference-DOI: 10.1016/J.JMB.2011.11.012

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UHRF1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 299-364
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INVERTED CCAAT BOX-BINDING PROTEIN OF 90 KDA, NUCLEAR PROTEIN 95, NUCLEAR ZINC FINGER PROTEIN NP95, HUNP95, RING FINGER PROTEIN 106, TRANSCRIPTION FACTOR ICBP90, UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN-CONTAINING PROTEIN 1, UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN 1

Molecule 2 - HISTONE H3.1T N-TERMINAL PEPTIDE
	Chains	:	D
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	H3/T, H3T, H3/G
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:302 , CYS A:305 , CYS A:313 , CYS A:316	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	CYS A:318 , CYS A:321 , HIS A:341 , CYS A:344	BINDING SITE FOR RESIDUE ZN A 2
3	AC3	SOFTWARE	CYS A:333 , CYS A:336 , CYS A:360 , CYS A:363	BINDING SITE FOR RESIDUE ZN A 3
4	AC4	SOFTWARE	HOH A:57 , HIS A:319 , GLU A:362 , HIS B:304	BINDING SITE FOR RESIDUE ZN A 8
5	AC5	SOFTWARE	ASP A:334 , ASP A:356 , ASP B:356	BINDING SITE FOR RESIDUE MG A 365
6	AC6	SOFTWARE	CYS B:302 , CYS B:305 , CYS B:313 , CYS B:316	BINDING SITE FOR RESIDUE ZN B 4
7	AC7	SOFTWARE	CYS B:318 , CYS B:321 , HIS B:341 , CYS B:344	BINDING SITE FOR RESIDUE ZN B 5
8	AC8	SOFTWARE	CYS B:333 , CYS B:336 , CYS B:360 , CYS B:363	BINDING SITE FOR RESIDUE ZN B 6
9	AC9	SOFTWARE	GLU A:297 , HIS A:304 , HIS B:319 , GLU B:362	BINDING SITE FOR RESIDUE ZN B 7

(no "SS Bond" information available for 3T6R)

Asymmetric Unit

No.	Residues
1	Asp A:346	-	Pro A:347
2	Gly B:299	-	Pro B:300
3	Asp B:346	-	Pro B:347

(no "SAP(SNP)/Variant" information available for 3T6R)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	2	A:302-363 B:302-363
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	2	A:310-364 B:310-364
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	2	A:318-364 B:318-364 -

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	A:302-363 -
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	1	A:310-364 -
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	1	A:318-364 - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	- B:302-363
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	1	- B:310-364
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	1	- B:318-364 -

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000366696	1	ENSE00001442338	chr1:228613026-228612546	481	H31T_HUMAN	1-136	136	1	D:1-5	5

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
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Chain A from PDB  Type:PROTEIN  Length:70
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:83
                                   291       301       311       321       331       341       351       361   
          UHRF1_HUMAN   282 RPGEGSPMVDNPMRRKSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 364
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------.............................hhh.eee......eee....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------ZF_PHD_1  PDB: A:302-363 UniProt: 302-363                     - PROSITE (1)
                PROSITE (2) ----------------------------ZF_PHD_2  PDB: A:310-364 UniProt: 310-366               PROSITE (2)
                PROSITE (3) ------------------------------------ZF_RING_2  PDB: A:318-364 UniProt: 318-364      PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 3t6r A 295 AP-------------EFGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 364
                             |       -     | 301       311       321       331       341       351       361   
                           296           297

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:68
                                   306       316       326       336       346       356        
          UHRF1_HUMAN   297 KSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 364
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................hhh.eee......eee.hhh................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ZF_PHD_1  PDB: B:302-363 UniProt: 302-363                     - PROSITE (1)
                PROSITE (2) -------------ZF_PHD_2  PDB: B:310-364 UniProt: 310-366               PROSITE (2)
                PROSITE (3) ---------------------ZF_RING_2  PDB: B:318-364 UniProt: 318-364      PROSITE (3)
                 Transcript -------------------------------------------------------------------- Transcript
                 3t6r B 297 EFGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 364
                                   306       316       326       336       346       356

Chain D from PDB  Type:PROTEIN  Length:5
 aligned with H31T_HUMAN | Q16695 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:5
           H31T_HUMAN     2 ARTKQ   6
               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   Transcript 1
                 3t6r D   1 ARTKQ   5

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 3T6R)

(no "CATH Domain" information available for 3T6R)

(no "Pfam Domain" information available for 3T6R)

Asymmetric Unit(hide GO term definitions)

Chain A,B (UHRF1_HUMAN | Q96T88)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000987	core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
	GO:0044729	hemi-methylated DNA-binding	Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008327	methyl-CpG binding	Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
	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:0031493	nucleosomal histone binding	Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
	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:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	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:0010390	histone monoubiquitination	The modification of histones by addition of a single ubiquitin group.
	GO:0016574	histone ubiquitination	The modification of histones by addition of ubiquitin groups.
	GO:0010216	maintenance of DNA methylation	Any process involved in maintaining the methylation state of a nucleotide sequence.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:2000373	positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	Any process that activates or increases the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity.
	GO:0032270	positive regulation of cellular protein metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
	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:0051865	protein autoubiquitination	The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0090308	regulation of methylation-dependent chromatin silencing	Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
	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:0000791	euchromatin	A dispersed and relatively uncompacted form of chromatin.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	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:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

Chain D (H31T_HUMAN | Q16695)

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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	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:0032460	negative regulation of protein oligomerization	Any process that stops, prevents, or reduces the frequency, rate or extent of protein oligomerization.
	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: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.
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:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	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.

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		Gly B:299 - Pro B:300	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3T6R)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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