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Description

Title :   SOLUTION STRUCTURE OF THE MYB-LIKE DNA-BINDING DOMAIN OF HUMAN ZZZ3 PROTEIN

Authors :   H. Abe, N. Tochio, K. Miyamoto, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   06 Apr 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Transcription, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Abe, N. Tochio, K. Miyamoto, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Myb-Like Dna-Binding Domain Of Human Zzz3 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - ZINC FINGER ZZ-TYPE-CONTAINING PROTEIN 3
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050613-19
	Expression System Vector Type	:	PLASMID
	Fragment	:	MYB-LIKE DNA-BINDING DOMAIN, UNP RESIDUES 652- 713
	Gene	:	ZZZ3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	ZZZ3 PROTEIN

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2YUM)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MYB	PS51294	Myb-type HTH DNA-binding domain profile.	ZZZ3_HUMAN	647-707	1	A:8-63

Exons (5, 5)

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000370801	2b	ENSE00001374496	chr1:78148343-78148270	74	ZZZ3_HUMAN	-	0	0	-	-
1.4	ENST00000370801	4	ENSE00001381493	chr1:78107340-78107207	134	ZZZ3_HUMAN	-	0	0	-	-
1.5a	ENST00000370801	5a	ENSE00001372837	chr1:78107131-78107069	63	ZZZ3_HUMAN	-	0	0	-	-
1.6	ENST00000370801	6	ENSE00002161656	chr1:78105287-78105134	154	ZZZ3_HUMAN	-	0	0	-	-
1.7d	ENST00000370801	7d	ENSE00001453662	chr1:78099090-78097535	1556	ZZZ3_HUMAN	1-502	502	0	-	-
1.9	ENST00000370801	9	ENSE00001184000	chr1:78050340-78050202	139	ZZZ3_HUMAN	502-548	47	0	-	-
1.10	ENST00000370801	10	ENSE00001183997	chr1:78047811-78047664	148	ZZZ3_HUMAN	549-598	50	0	-	-
1.11a	ENST00000370801	11a	ENSE00001183994	chr1:78047576-78047461	116	ZZZ3_HUMAN	598-636	39	1	A:1-6	6
1.12b	ENST00000370801	12b	ENSE00001317615	chr1:78046754-78046683	72	ZZZ3_HUMAN	637-660	24	1	A:7-16 (gaps)	21
1.12d	ENST00000370801	12d	ENSE00001184005	chr1:78045313-78045212	102	ZZZ3_HUMAN	661-694	34	1	A:17-50	34
1.13	ENST00000370801	13	ENSE00001066865	chr1:78044554-78044459	96	ZZZ3_HUMAN	695-726	32	1	A:51-72 (gaps)	24
1.14	ENST00000370801	14	ENSE00001066866	chr1:78041905-78041753	153	ZZZ3_HUMAN	727-777	51	1	A:73-75	3
1.15	ENST00000370801	15	ENSE00001013626	chr1:78034151-78034017	135	ZZZ3_HUMAN	778-822	45	0	-	-
1.16	ENST00000370801	16	ENSE00001013627	chr1:78031866-78031766	101	ZZZ3_HUMAN	823-856	34	0	-	-
1.17c	ENST00000370801	17c	ENSE00001859472	chr1:78031469-78030185	1285	ZZZ3_HUMAN	856-903	48	0	-	-

Sequences/Alignments

NMR Structure

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:75
 aligned with ZZZ3_HUMAN | Q8IYH5 from UniProtKB/Swiss-Prot  Length:903

    Alignment length:103
                                   636       646       656       666       676       686       696       706       716       726   
           ZZZ3_HUMAN   627 GPEGSSSRPQMIRGRLCDDTKPETFNQLWTVEEQKKLEQLLIKYPPEEVESRRWQKIADELGNRTAKQVASRVQKYFIKLTKAGIPVPGRTPNLYIYSKKSST 729
               SCOP domains d2yuma       _            A: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------Myb_DNA-binding-2yumA01 A:8-59                      -------------------------- Pfam domains
         Sec.struct. author ......-------.-----------....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........--.--------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------HTH_MYB  PDB: A:8-63 UniProt: 647-707                        ---------------------- PROSITE
               Transcript 1 Exon 1.11aExon 1.12b [INCOMPLETE] Exon 1.12d  PDB: A:17-50          Exon 1.13  PDB: A:51-72 (gaps)  1.1 Transcript 1
                 2yum A   1 GSSGSS-------G-----------NQLWTVEEQKKLEQLLIKYPPEEVESRRWQKIADELGNRTAKQVASQVQKYFIKLTKAGIPVSG--P--------SSG  75
                                 |   -   |     -     |  12        22        32        42        52        62        |- |       -|  
                                 6       7           8                                                             71 72       73

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Homeodomain-like (373)

Family: automated matches (53)

Protein domain: automated matches (53)

Human (Homo sapiens) [TaxId: 9606] (19)

d2yuma_

CATH Domains (0, 0)

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

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Myb_DNA-binding (17)

Homo sapiens (Human) (17)

Myb_DNA-binding-2yumA01

A:8-59

Gene Ontology (9, 9)

NMR Structure(hide GO term definitions)

Chain A (ZZZ3_HUMAN | Q8IYH5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0005671	Ada2/Gcn5/Ada3 transcription activator complex	A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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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Related Entries

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	ZZZ3_HUMAN \| Q8IYH5	:	2fc7

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