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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

Authors :   M. Okuda, Y. Watanabe, H. Okamura, F. Hanaoka, Y. Ohkuma, Y. Nishimura, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   25 Oct 99 (Deposition) - 26 Apr 00 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   Winged Helix-Turn-Helix, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Okuda, Y. Watanabe, H. Okamura, F. Hanaoka, Y. Ohkuma, Y. Nishimura
Structure Of The Central Core Domain Of Tfiiebeta With A Novel Double-Stranded Dna-Binding Surface.
Embo J. V. 19 1346 2000
PubMed-ID: 10716934 | Reference-DOI: 10.1093/EMBOJ/19.6.1346
(for further references see the PDB file header)

Molecule 1 - GENERAL TRANSCRIPTION FACTOR TFIIE-BETA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Taxid	:	562
	Fragment	:	CENTRAL CORE DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1D8K)

(no "Site" information available for 1D8K)

(no "SS Bond" information available for 1D8K)

(no "Cis Peptide Bond" information available for 1D8K)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052281	I	133	T	T2EB_HUMAN	Polymorphism	2229299	A	I	68	T

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIIE_BETA_C	PS51351	TFIIE beta central core DNA-binding domain profile.	T2EB_HUMAN	66-146	1	A:1-81

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000355904	1a	ENSE00001374568	chr8:30515768-30515490	279	T2EB_HUMAN	-	0	0	-	-
1.4	ENST00000355904	4	ENSE00001092687	chr8:30511119-30510950	170	T2EB_HUMAN	1-56	56	0	-	-
1.7	ENST00000355904	7	ENSE00000687890	chr8:30492640-30492549	92	T2EB_HUMAN	56-86	31	1	A:1-21	21
1.8	ENST00000355904	8	ENSE00000687887	chr8:30472232-30472125	108	T2EB_HUMAN	87-122	36	1	A:22-57	36
1.9b	ENST00000355904	9b	ENSE00001158778	chr8:30469998-30469816	183	T2EB_HUMAN	123-183	61	1	A:58-81	24
1.10b	ENST00000355904	10b	ENSE00000687877	chr8:30464667-30464574	94	T2EB_HUMAN	184-215	32	0	-	-
1.13	ENST00000355904	13	ENSE00000687873	chr8:30437913-30437798	116	T2EB_HUMAN	215-253	39	0	-	-
1.14	ENST00000355904	14	ENSE00001092688	chr8:30436554-30435835	720	T2EB_HUMAN	254-291	38	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

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Chain A from PDB  Type:PROTEIN  Length:81
 aligned with T2EB_HUMAN | P29084 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:81
                                    75        85        95       105       115       125       135       145 
           T2EB_HUMAN    66 ALSGSSGYKFGVLAKIVNYMKTRHQRGDTHPLTLDEILDETQHLDIGLKQKQWLMTEALVNNPKIEVIDGKYAFKPKYNVR 146
               SCOP domains d1d8ka_ A: The central core domain of TFIIE beta                                  SCOP domains
               CATH domains 1d8kA00 A:1-81 'winged helix' repressor DNA binding domain                        CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh......e.hhhhhhh.......hhhhhhhh.........eeee..eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------T------------- SAPs(SNPs)
                    PROSITE TFIIE_BETA_C  PDB: A:1-81 UniProt: 66-146                                         PROSITE
               Transcript 1 Exon 1.7  PDB: A:1-21Exon 1.8  PDB: A:22-57              Exon 1.9b  PDB: A:58-81  Transcript 1
                 1d8k A   1 ALSGSSGYKFGVLAKIVNYMKTRHQRGDTHPLTLDEILDETQHLDIGLKQKQWLMTEALVNNPKIEVIDGKYAFKPKYNVR  81
                                    10        20        30        40        50        60        70        80

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: All alpha proteins (14657)

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

Superfamily: Winged helix DNA-binding domain (576)

Family: The central core domain of TFIIE beta (2)

Protein domain: The central core domain of TFIIE beta (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1d8ka_

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Human (Homo sapiens) (70)

1d8kA00

A:1-81

(no "Pfam Domain" information available for 1D8K)

NMR Structure(hide GO term definitions)

Chain A (T2EB_HUMAN | P29084)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	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:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of 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.
	GO:0005673	transcription factor TFIIE complex	A transcription factor which in humans consists of a complex of two alpha and two beta chains. Recruits TFIIH to the initiation complex and helps activate both RNA polymerase II and TFIIH.

NMR Structure
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	T2EB_HUMAN \| P29084	:	1d8j 5gpy 5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd

1d8j	RELATED ID: TRT001000206.1 RELATED DB: TARGETDB

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