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Title :   SOLUTION STRUCTURE OF A COMPLEX OF THE THIRD DNA BINDING DOMAIN OF HUMAN HMG-I(Y) BOUND TO DNA DODECAMER CONTAINING THE PRDII SITE OF THE INTERFERON-BETA PROMOTER, NMR, MINIMIZED AVERAGE STRUCTURE

Authors :   G. M. Clore, J. R. Huth, C. Bewley, A. M. Gronenborn

Date :   04 Jun 97 (Deposition) - 15 Oct 97 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C

Keywords :   Dna Binding Protein, Minor Groove Dna Binding, Transcriptional Co-Activator, Architectural Factor, Complex (Dna-Binding Protein/Dna), Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Huth, C. A. Bewley, M. S. Nissen, J. N. Evans, R. Reeves, A. M. Gronenborn, G. M. Clore
The Solution Structure Of An Hmg-I(Y)-Dna Complex Defines A New Architectural Minor Groove Binding Motif.
Nat. Struct. Biol. V. 4 657 1997
PubMed-ID: 9253416 | Reference-DOI: 10.1038/NSB0897-657
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(GPGPGPAPAPAPTPTPCPCPTPC)- 3')*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(GPAPGPGPAPAPTPTPTPCPCPC)- 3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-Y
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HIGH MOBILITY GROUP PROTEIN HMG


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2EZF)

(no "Site" information available for 2EZF)

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

(no "Cis Peptide Bond" information available for 2EZF)

(no "SAP(SNP)/Variant" information available for 2EZF)

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

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000311487	1a	ENSE00001175366	chr6:34204577-34204740	164	HMGA1_HUMAN	-	0	0	-	-
1.1d	ENST00000311487	1d	ENSE00001032854	chr6:34204981-34205094	114	HMGA1_HUMAN	-	0	0	-	-
1.4b	ENST00000311487	4b	ENSE00001160563	chr6:34208514-34208692	179	HMGA1_HUMAN	1-45	45	0	-	-
1.5c	ENST00000311487	5c	ENSE00002147279	chr6:34210489-34210572	84	HMGA1_HUMAN	46-73	28	0	-	-
1.6	ENST00000311487	6	ENSE00002166227	chr6:34211245-34211295	51	HMGA1_HUMAN	74-90	17	1	A:32-41	10
1.7b	ENST00000311487	7b	ENSE00002149717	chr6:34212608-34214007	1400	HMGA1_HUMAN	91-107	17	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:10
 aligned with HMGA1_HUMAN | P17096 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:10
                                    89
          HMGA1_HUMAN    80 GRKPRGRPKK  89
               SCOP domains d2ezfa_ A: SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.6   Transcript 1
                 2ezf A  32 GRKPRGRPKK  41
                                    41

Chain B from PDB  Type:DNA  Length:12
                                            
                 2ezf B 301 GGGAAATTCCTC 312
                                   310

Chain C from PDB  Type:DNA  Length:12
                                            
                 2ezf C 313 GAGGAATTTCCC 324
                                   322

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Peptides (792)

Fold: DNA-binding domains of HMG-I(Y) (4)

Superfamily: DNA-binding domains of HMG-I(Y) (4)

Family: DNA-binding domains of HMG-I(Y) (4)

Protein domain: DNA-binding domains of HMG-I(Y) (4)

Human (Homo sapiens) [TaxId: 9606] (4)

d2ezfa_

(no "CATH Domain" information available for 2EZF)

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

NMR Structure(hide GO term definitions)

Chain A (HMGA1_HUMAN | P17096)

molecular function
	GO:0051575	5'-deoxyribose-5-phosphate lyase activity	Catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site.
	GO:0003680	AT DNA binding	Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003906	DNA-(apurinic or apyrimidinic site) lyase activity	Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
	GO:0042975	peroxisome proliferator activated receptor binding	Interacting selectively and non-covalently with any of the peroxisome proliferator activated receptors, alpha, beta or gamma.
	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:0042974	retinoic acid receptor binding	Interacting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily.
	GO:0046965	retinoid X receptor binding	Interacting selectively and non-covalently with a retinoid X receptor.
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0001205	transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0006268	DNA unwinding involved in DNA replication	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0031936	negative regulation of chromatin silencing	Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0051169	nuclear transport	The directed movement of substances into, out of, or within the nucleus.
	GO:0006337	nucleosome disassembly	The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0090402	oncogene-induced cell senescence	A cellular senescence process associated with the dismantling of a cell as a response to oncogenic stress, such as the activation of the Ras oncogenic family.
	GO:2000774	positive regulation of cellular senescence	Any process that activates or increases the frequency, rate or extent of cellular senescence.
	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:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
	GO:0035986	senescence-associated heterochromatin focus assembly	The assembly of chromatin into senescence-associated heterochromatin foci (SAHF), transcriptionally-silent heterochromatin structures present in senescent cells, containing the condensed chromatin of one chromosome, and enriched for histone modifications. Formation of these chromatin structures is thought to repress expression of proliferation-promoting genes.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0090575	RNA polymerase II transcription factor complex	A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	GO:0035985	senescence-associated heterochromatin focus	A transcriptionally-silent heterochromatin structure present in senescent cells. Contains the condensed chromatin of one chromosome and is enriched for histone modifications. Thought to repress expression of proliferation-promoting genes.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

NMR Structure
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	2ezf
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	HMGA1_HUMAN \| P17096	:	2ezd 2eze 2ezg

2ezg	ENSEMBLE OF 35 STRUCTURES

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