1DL6 - JenaLib

NMR Structure - manually (Jmol Viewer)

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN

Authors :   H. -T. Chen, P. Legault, J. Glushka, J. G. Omichinski, R. A. Scott

Date :   08 Dec 99 (Deposition) - 18 Oct 00 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (25x)

Keywords :   Zinc Ribbon, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. T. Chen, P. Legault, J. Glushka, J. G. Omichinski, R. A. Scott
Structure Of A (Cys3His) Zinc Ribbon, A Ubiquitous Motif In Archaeal And Eucaryal Transcription.
Protein Sci. V. 9 1743 2000
PubMed-ID: 11045620
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION FACTOR II B (TFIIB)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (25x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

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

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:15 , HIS A:18 , CYS A:34 , CYS A:37	BINDING SITE FOR RESIDUE ZN A 60

(no "SS Bond" information available for 1DL6)

(no "Cis Peptide Bond" information available for 1DL6)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011977	P	19	S	TF2B_HUMAN	Polymorphism	1804499	A	P	19	S

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_TFIIB	PS51134	Zinc finger TFIIB-type profile.	TF2B_HUMAN	11-42	1	A:11-42

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000370500	1c	ENSE00001452875	chr1:89357301-89357166	136	TF2B_HUMAN	1-6	6	1	A:2-6	5
1.3b	ENST00000370500	3b	ENSE00001158820	chr1:89353050-89352944	107	TF2B_HUMAN	6-42	37	1	A:6-42	37
1.4c	ENST00000370500	4c	ENSE00000932079	chr1:89329797-89329664	134	TF2B_HUMAN	42-86	45	1	A:42-59	18
1.5a	ENST00000370500	5a	ENSE00000932078	chr1:89325969-89325823	147	TF2B_HUMAN	87-135	49	0	-	-
1.6	ENST00000370500	6	ENSE00000932077	chr1:89325694-89325565	130	TF2B_HUMAN	136-179	44	0	-	-
1.8d	ENST00000370500	8d	ENSE00000932076	chr1:89323170-89322889	282	TF2B_HUMAN	179-273	95	0	-	-
1.9b	ENST00000370500	9b	ENSE00001158811	chr1:89319029-89318615	415	TF2B_HUMAN	273-316	44	0	-	-

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:58
 aligned with TF2B_HUMAN | Q00403 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:58
                                    11        21        31        41        51        
            TF2B_HUMAN    2 ASTSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDK 59
               SCOP domains d1dl6a_ A:                                                 SCOP domains
               CATH domains 1dl6A00 A:2-59  [code=2.20.25.10, no name defined]         CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee......ee......ee.................. Sec.struct. author
                 SAPs(SNPs) -----------------S---------------------------------------- SAPs(SNPs)
                    PROSITE ---------ZF_TFIIB  PDB: A:11-42          ----------------- PROSITE
           Transcript 1 (1) 1.1c -----------------------------------Exon 1.4c          Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.3b  PDB: A:6-42 UniProt: 6-42 ----------------- Transcript 1 (2)
                  1dl6 A  2 ASTSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDK 59
                                    11        21        31        41        51

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: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Zinc beta-ribbon (41)

Family: Transcriptional factor domain (36)

Protein domain: Transcription initiation factor TFIIB, N-terminal domain (4)

Human (Homo sapiens) [TaxId: 9606] (3)

d1dl6a_

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 Beta (13760)

Architecture: Single Sheet (341)

Topology: N-terminal domain of TfIIb (166)

Homologous Superfamily: [code=2.20.25.10, no name defined] (79)

Human (Homo sapiens) (5)

1dl6A00

A:2-59

(no "Pfam Domain" information available for 1DL6)

NMR Structure(hide GO term definitions)

Chain A (TF2B_HUMAN | Q00403)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0017025	TBP-class protein binding	Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
	GO:0001047	core promoter binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	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:0046966	thyroid hormone receptor binding	Interacting selectively and non-covalently with a thyroid hormone receptor.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core 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. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	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: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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	TF2B_HUMAN \| Q00403	:	1c9b 1rly 1ro4 1tfb 1vol 2phg 5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd

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