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Description

Title :   SOLUTION STRUCTURE OF TRASH DOMAIN OF ZINC FINGER MYM-TYPE PROTEIN 5

Authors :   T. N. Niraula, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   14 Dec 05 (Deposition) - 14 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Trash Domain, Zinc Finger Mym-Type Protein 5, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. N. Niraula, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of Trash Domain Of Zinc Finger Mym-Type Protein 5
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - ZINC FINGER MYM-TYPE PROTEIN 5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050322-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRASH DOMAIN
	Gene	:	ZMYM5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	ZINC FINGER PROTEIN 237, ZINC FINGER PROTEIN 198- LIKE 1

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

Sites (1, 1)

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:23 , CYS A:26 , CYS A:47 , CYS A:51	BINDING SITE FOR RESIDUE ZN A 101

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_062160	T	231	A	ZMYM5_HUMAN	Polymorphism	41292167	A	T	10	A

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

PROSITE Motifs (0, 0)

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

Exons (1, 1)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000337963	1a	ENSE00001229583	chr13:20437776-20437590	187	ZMYM5_HUMAN	-	0	0	-	-
1.2	ENST00000337963	2	ENSE00000994960	chr13:20436606-20436539	68	ZMYM5_HUMAN	-	0	0	-	-
1.3a	ENST00000337963	3a	ENSE00001637679	chr13:20426330-20425829	502	ZMYM5_HUMAN	1-164	164	0	-	-
1.3d	ENST00000337963	3d	ENSE00001795699	chr13:20425588-20425495	94	ZMYM5_HUMAN	165-196	32	0	-	-
1.4	ENST00000337963	4	ENSE00001619792	chr13:20413125-20412840	286	ZMYM5_HUMAN	196-291	96	1	A:1-62 (gaps)	84
1.5a	ENST00000337963	5a	ENSE00001493770	chr13:20411961-20411796	166	ZMYM5_HUMAN	291-346	56	0	-	-
1.6	ENST00000337963	6	ENSE00001758181	chr13:20409829-20409617	213	ZMYM5_HUMAN	347-417	71	0	-	-
1.7a	ENST00000337963	7a	ENSE00001541459	chr13:20399375-20397624	1752	ZMYM5_HUMAN	418-669	252	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:62
 aligned with ZMYM5_HUMAN | Q9UJ78 from UniProtKB/Swiss-Prot  Length:669

    Alignment length:84
                                   209       219       229       239       249       259       269       279    
          ZMYM5_HUMAN   200 SQSASFPSNQKQPGVDSLSPVALLRKQNFQPTAQQQLTKPAKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSHKRTQN 283
               SCOP domains ---------d                    2dasa1 A:8-56 Zinc finger MYM-type protein 5    ------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....--...--------------------............................ee......ee.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------A---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4  PDB: A:1-62 (gaps) UniProt: 196-291 [INCOMPLETE]                           Transcript 1
                 2das A   1 GSSGS--SGQ--------------------PTAQQQLTKPAKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSSGPSSG  62
                                |  | 8         -         -|       18        28        38        48        58    
                                5  6 8                    9

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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: Small proteins (3458)

Fold: Glucocorticoid receptor-like (DNA-binding domain) (292)

Superfamily: Glucocorticoid receptor-like (DNA-binding domain) (292)

Family: TRASH domain (1)

Protein domain: Zinc finger MYM-type protein 5 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2dasa1

A:8-56

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (12, 12)

NMR Structure(hide GO term definitions)

Chain A (ZMYM5_HUMAN | Q9UJ78)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	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:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (1, 1)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (12, 12)

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