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Title :   COMPLEX STRUCTURE OF THE C-TERMINAL RNA-BINDING DOMAIN OF HNRNP D (AUF1) WITH TELOMERE DNA

Authors :   Y. Enokizono, Y. Konishi, K. Nagata, K. Ouhashi, S. Uesugi, F. Ishikawa, M. Katahira

Date :   22 Nov 04 (Deposition) - 05 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Rna-Binding Domain, Dna-Binding Domain, Rrm, Hnrnp D, Auf1, Telomere, Complex, Structural Genomics, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Enokizono, Y. Konishi, K. Nagata, K. Ouhashi, S. Uesugi, F. Ishikawa, M. Katahira
Structure Of Hnrnp D Complexed With Single-Stranded Telomere Dna And Unfolding Of The Quadruplex By Heterogeneous Nuclear Ribonucleoprotein D
J. Biol. Chem. V. 280 18862 2005
PubMed-ID: 15734733 | Reference-DOI: 10.1074/JBC.M411822200
(for further references see the PDB file header)

Molecule 1 - HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL RNA-BINDING DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	AUF1, HNRNP D0, AU-RICH ELEMENT RNA-BINDING PROTEIN 1

*Molecule 2 - 5'-D(PTPAPGPG)-3'*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1WTB)

(no "Site" information available for 1WTB)

(no "SS Bond" information available for 1WTB)

(no "Cis Peptide Bond" information available for 1WTB)

(no "SAP(SNP)/Variant" information available for 1WTB)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	HNRPD_HUMAN	97-179 182-261	1	- A:182-259

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3e	ENST00000313899	3e	ENSE00001843674	chr4:83295109-83294599	511	HNRPD_HUMAN	1-78	78	0	-	-
1.5	ENST00000313899	5	ENSE00001181831	chr4:83292737-83292681	57	HNRPD_HUMAN	78-97	20	0	-	-
1.6b	ENST00000313899	6b	ENSE00001251874	chr4:83280792-83280624	169	HNRPD_HUMAN	97-153	57	0	-	-
1.7c	ENST00000313899	7c	ENSE00001181862	chr4:83279973-83279812	162	HNRPD_HUMAN	154-207	54	1	A:181-207	27
1.7f	ENST00000313899	7f	ENSE00001251906	chr4:83278597-83278466	132	HNRPD_HUMAN	208-251	44	1	A:208-251	44
1.8a	ENST00000313899	8a	ENSE00001340965	chr4:83278048-83277949	100	HNRPD_HUMAN	252-285	34	1	A:252-259	8
1.8d	ENST00000313899	8d	ENSE00001127181	chr4:83277836-83277690	147	HNRPD_HUMAN	285-334	50	0	-	-
1.8e	ENST00000313899	8e	ENSE00001251846	chr4:83276554-83276457	98	HNRPD_HUMAN	334-355	22	0	-	-
1.8k	ENST00000313899	8k	ENSE00002072421	chr4:83275307-83273651	1657	HNRPD_HUMAN	-	0	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:79
 aligned with HNRPD_HUMAN | Q14103 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:79
                                   190       200       210       220       230       240       250         
          HNRPD_HUMAN   181 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMS 259
               SCOP domains d1wtba_ A: automated matches                                                    SCOP domains
               CATH domains 1wtbA00 A:181-259  [code=3.30.70.330, no name defined]                          CATH domains
               Pfam domains ---RRM_1-1wtbA01 A:184-254                                                ----- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhh..eeeeeee..........eeeeee..hhhhhhhhh..eeee..eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RRM  PDB: A:182-259 UniProt: 182-261                                           PROSITE
               Transcript 1 Exon 1.7c  PDB: A:181-207  Exon 1.7f  PDB: A:208-251 UniProt: 208-251  1.8a     Transcript 1
                 1wtb A 181 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMS 259
                                   190       200       210       220       230       240       250

Chain B from PDB  Type:DNA  Length:4
                                    
                 1wtb B   2 TAGG   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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: automated matches (24)

Human (Homo sapiens) [TaxId: 9606] (21)

d1wtba_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

Human (Homo sapiens) (81)

1wtbA00

A:181-259

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Homo sapiens (Human) (94)

RRM_1-1wtbA01

A:184-254

NMR Structure(hide GO term definitions)

Chain A (HNRPD_HUMAN | Q14103)

molecular function
	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:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0035925	mRNA 3'-UTR AU-rich region binding	Interacting selectively and non-covalently with a region containing frequent adenine and uridine bases within the 3' untranslated region of a mRNA molecule.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0061158	3'-UTR-mediated mRNA destabilization	An mRNA destabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA.
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0071230	cellular response to amino acid 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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
	GO:0071392	cellular response to estradiol 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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0071732	cellular response to nitric oxide	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 nitric oxide stimulus.
	GO:1904586	cellular response to putrescine	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 putrescine stimulus.
	GO:0021549	cerebellum development	The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
	GO:0097167	circadian regulation of translation	Any process that modulates the frequency, rate or extent of mRNA translation with a regularity of approximately 24 hours.
	GO:0010467	gene expression	The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1990828	hepatocyte dedifferentiation	The process in which a hepatocyte (specialized epithelial cell of the liver) loses the structural or functional features that characterize it in the mature organism, or some other relatively stable phase of the organism's life history. Under certain conditions, these cells can revert back to the features of the stem cells that were their ancestors.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0048255	mRNA stabilization	Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0042752	regulation of circadian rhythm	Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0051592	response to calcium ion	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 calcium ion stimulus.
	GO:0051602	response to electrical stimulus	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 an electrical stimulus.
	GO:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0014076	response to fluoxetine	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 fluoxetine stimulus. Fluoxetine increases the extracellular level of the neurotransmitter serotonin by inhibiting its reuptake into the presynaptic cell, increasing the level of serotonin available to bind to the postsynaptic receptor.
	GO:1901355	response to rapamycin	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 rapamycin stimulus.
	GO:1904383	response to sodium phosphate	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 sodium phosphate stimulus.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	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.

NMR Structure
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	HNRPD_HUMAN \| Q14103	:	1hd0 1hd1 1iqt 1x0f 2z5n 5im0

1hd0	THE MINIMIZED AVERAGE STRUCTURE OF THE N-TERMINAL RNA- BINDING DOMAIN OF HNRNP D
1hd1	THE 20 STRUCTURES OF THE N-TERMINAL RNA-BINDING DOMAIN OF HNRNP D
1iqt	THE 20 STRUCTURES WITH THE LOWEST ENAGEY OF THE C-TERMINAL RNA-BINDING DOMAIN OF HNRNP D

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