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NMR Structure - model 1

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NMR Structure - model 1 (Jmol Viewer)

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Description

Title :   SOLUTION STRUCTURE OF RSGI RUH-067, A GTF2I DOMAIN IN HUMAN CDNA

Authors :   Y. Doi-Katayama, H. Hirota, Y. Muto, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Sep 06 (Deposition) - 30 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Rsgi Ruh-067, Transcription Factor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Doi-Katayama, H. Hirota, Y. Muto, S. Yokoyama
Solution Structure Of Rsgi Ruh-067, A Gtf2I Domain In Human Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - GENERAL TRANSCRIPTION FACTOR II-I REPEAT DOMAIN- CONTAINING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050627-07
	Expression System Vector Type	:	PLASMID
	Fragment	:	GTF2I DOMAIN, GTF2I-LIKE 4
	Gene	:	NP005676
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS (E. COLI)
	Synonym	:	GTF2I REPEAT DOMAIN-CONTAINING PROTEIN 1, MUSCLE TFII-I REPEAT DOMAIN-CONTAINING PROTEIN 1, GENERAL TRANSCRIPTION FACTOR III, SLOW- MUSCLE-FIBER ENHANCER- BINDING PROTEIN, USE B1-BINDING PROTEIN, MUSTRD1/BEN, WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 11 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 2DZR)

Sites (0, 0)

(no "Site" information available for 2DZR)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 2)

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GTF2I	PS51139	GTF2I-like repeat profile.	GT2D1_HUMAN	119-213 342-436 556-650 696-790 793-887	2	- - - A:8-93 A:95-99

Exons (7, 7)

NMR Structure (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000265755	1a	ENSE00001341217	chr7:73868120-73868506	387	GT2D1_HUMAN	-	0	0	-	-
1.3	ENST00000265755	3	ENSE00002196204	chr7:73922405-73922533	129	GT2D1_HUMAN	1-41	41	0	-	-
1.4	ENST00000265755	4	ENSE00000691482	chr7:73927160-73927301	142	GT2D1_HUMAN	42-89	48	0	-	-
1.5b	ENST00000265755	5b	ENSE00000691481	chr7:73929771-73929926	156	GT2D1_HUMAN	89-141	53	0	-	-
1.6	ENST00000265755	6	ENSE00000403997	chr7:73932469-73932652	184	GT2D1_HUMAN	141-202	62	0	-	-
1.7	ENST00000265755	7	ENSE00000691478	chr7:73933739-73934049	311	GT2D1_HUMAN	202-306	105	0	-	-
1.8	ENST00000265755	8	ENSE00000403999	chr7:73935538-73935627	90	GT2D1_HUMAN	306-336	31	0	-	-
1.9	ENST00000265755	9	ENSE00000404000	chr7:73938401-73938484	84	GT2D1_HUMAN	336-364	29	0	-	-
1.10	ENST00000265755	10	ENSE00000404001	chr7:73944064-73944247	184	GT2D1_HUMAN	364-425	62	0	-	-
1.11	ENST00000265755	11	ENSE00001039150	chr7:73949443-73949468	26	GT2D1_HUMAN	425-434	10	0	-	-
1.12	ENST00000265755	12	ENSE00000843247	chr7:73950497-73950605	109	GT2D1_HUMAN	434-470	37	0	-	-
1.13	ENST00000265755	13	ENSE00001735710	chr7:73952466-73952503	38	GT2D1_HUMAN	470-483	14	0	-	-
1.14	ENST00000265755	14	ENSE00000691417	chr7:73953010-73953090	81	GT2D1_HUMAN	483-510	28	0	-	-
1.15	ENST00000265755	15	ENSE00001713711	chr7:73954209-73954298	90	GT2D1_HUMAN	510-540	31	0	-	-
1.16	ENST00000265755	16	ENSE00001704452	chr7:73959085-73959132	48	GT2D1_HUMAN	540-556	17	0	-	-
1.17a	ENST00000265755	17a	ENSE00001603168	chr7:73960074-73960139	66	GT2D1_HUMAN	556-578	23	0	-	-
1.18	ENST00000265755	18	ENSE00001801491	chr7:73961433-73961616	184	GT2D1_HUMAN	578-639	62	0	-	-
1.19	ENST00000265755	19	ENSE00001716575	chr7:73969504-73969553	50	GT2D1_HUMAN	639-656	18	1	A:1-1	1
1.20a	ENST00000265755	20a	ENSE00001147974	chr7:73969723-73969824	102	GT2D1_HUMAN	656-690	35	1	A:1-7 (gaps)	20
1.21	ENST00000265755	21	ENSE00000691369	chr7:73971969-73972052	84	GT2D1_HUMAN	690-718	29	1	A:8-21	14
1.22	ENST00000265755	22	ENSE00000691365	chr7:73973191-73973374	184	GT2D1_HUMAN	718-779	62	1	A:21-82	62
1.23a	ENST00000265755	23a	ENSE00001039134	chr7:73973957-73973985	29	GT2D1_HUMAN	779-789	11	1	A:82-92	11
1.24	ENST00000265755	24	ENSE00001147952	chr7:74004180-74004257	78	GT2D1_HUMAN	789-815	27	1	A:92-95 (gaps)	27
1.25	ENST00000265755	25	ENSE00000404019	chr7:74005154-74005346	193	GT2D1_HUMAN	815-879	65	1	A:95-99	5
1.26	ENST00000265755	26	ENSE00001039136	chr7:74009341-74009378	38	GT2D1_HUMAN	879-892	14	0	-	-
1.27c	ENST00000265755	27c	ENSE00000691312	chr7:74015371-74015507	137	GT2D1_HUMAN	892-937	46	0	-	-
1.27f	ENST00000265755	27f	ENSE00001882339	chr7:74016692-74016917	226	GT2D1_HUMAN	938-959	22	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:99
 aligned with GT2D1_HUMAN | Q9UHL9 from UniProtKB/Swiss-Prot  Length:959

    Alignment length:164
                                   665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815    
          GT2D1_HUMAN   656 GTASSLGFSPPALPPERDSGDPLVDESLKRQGFQENYDARLSRIDIANTLREQVQDLFNKKYGEALGIKYPVQVPYKRIKSNPGSVIIEGLPPGIPFRKPCTFGSQNLERILAVADKIKFTVTRPFQGLIPKPDEDDANRLGEKVILREQVKELFNEKYGEALG 819
               SCOP domains d2dzr             a_                              A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------------..-----------------------------hhhhhhhhhhhhhhhhh..........hhhhh....eeee...............hhhhhhhhhh....eeee..............-----------------------..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------GTF2I  PDB: A:8-93 UniProt: 696-790                                                            --GTF2I  PDB: A:95-99         PROSITE
           Transcript 1 (1) 1---------------------------------Exon 1.21  PDB: A:8-21       ------------------------------------------------------------Exon 1.23a -------------------------1.25  Transcript 1 (1)
           Transcript 1 (2) Exon 1.20a  PDB: A:1-7 (gaps)      ---------------------------Exon 1.22  PDB: A:21-82 UniProt: 718-779                      ---------Exon 1.24 UniProt: 789-815 ---- Transcript 1 (2)
                 2dzr A   1 GSSGS-------------SG-----------------------------LREQVQDLFNKKYGEALGIKYPVQVPYKRIKSNPGSVIIEGLPPGIPFRKPCTFGSQNLERILAVADKIKFTVTRPFQGLIPKPDES-----------------------GPSSG  99
                                |    -        |7         -         -         8        18        28        38        48        58        68        78        88     |   -         -        95    
                                5             6|                             8                                                                                    94                      95    
                                               7

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

Fold: GTF2I-like repeat (9)

Superfamily: GTF2I-like repeat (9)

Family: automated matches (6)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (6)

d2dzra_

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (12, 12)

NMR Structure(hide GO term definitions)

Chain A (GT2D1_HUMAN | Q9UHL9)

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:0003705	transcription factor 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 modulate transcription by RNAP II.
	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.
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.
	GO:0014886	transition between slow and fast fiber	The process of conversion of slow-contracting muscle fibers to a faster character. This may involve increasing of contractile rate, fast myosin gene induction, increase in glycolytic metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
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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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	GT2D1_HUMAN \| Q9UHL9	:	2d99 2dn5 2dzq

Related Entries Specified in the PDB File

2d99	OTHER DOMAIN(RSGI RUH-048) FROM THE SAME PROTEIN RELATED ID: HSO002000922.3 RELATED DB: TARGETDB
2dn5	OTHER DOMAIN(RSGI RUH-057) FROM THE SAME PROTEIN
2dzq	OTHER DOMAIN(RSGI RUH-066) FROM THE SAME PROTEIN