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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE ZINC FINGER, C4-TYPE DOMAIN OF HUMAN COUP TRANSCRIPTION FACTOR 1

Authors :   M. Yoneyama, S. Koshiba, S. Watabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   09 Feb 07 (Deposition) - 19 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Dna-Binding, Metal-Binding, Nuclear Protein, Receptor, Transcription, Transcription Regulation, Zinc, Ear3, Erbal3, Tfcoup1, 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 :   M. Yoneyama, S. Koshiba, S. Watabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The Zinc Finger, C4-Type Domain Of Human Coup Transcription Factor 1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - COUP TRANSCRIPTION FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P051212-03
	Expression System Vector Type	:	PLASMID
	Fragment	:	ZINC FINGER, C4-TYPE
	Gene	:	NR2F1, EAR3, ERBAL3, TFCOUP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	COUP-TF1, COUP-TF I, V-ERBA-RELATED PROTEIN EAR-3


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:10 , CYS A:13 , CYS A:27 , CYS A:30	BINDING SITE FOR RESIDUE ZN A 191
2	AC2	SOFTWARE	CYS A:46 , CYS A:52 , CYS A:62 , CYS A:65	BINDING SITE FOR RESIDUE ZN A 241

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

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

NMR Structure (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071319	R	112	K	COT1_HUMAN	Disease (BBSOAS)	587777277	A	R	36	K
2	UniProt	VAR_071320	S	113	R	COT1_HUMAN	Disease (BBSOAS)	587777275	A	S	37	R
3	UniProt	VAR_071321	R	115	P	COT1_HUMAN	Disease (BBSOAS)	587777274	A	R	39	P

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

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUCLEAR_REC_DBD_2	PS51030	Nuclear hormone receptors DNA-binding domain profile.	COT1_HUMAN	83-158	1	A:8-82
2	NUCLEAR_REC_DBD_1	PS00031	Nuclear hormones receptors DNA-binding region signature.	COT1_HUMAN	86-112	1	A:10-36

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000327111	1	ENSE00001250011	chr5:92919043-92921192	2150	COT1_HUMAN	1-155	155	1	A:1-79 (gaps)	91
1.4c	ENST00000327111	4c	ENSE00001249995	chr5:92923623-92924150	528	COT1_HUMAN	155-331	177	1	A:79-89 (gaps)	15
1.6b	ENST00000327111	6b	ENSE00001250004	chr5:92929268-92930321	1054	COT1_HUMAN	331-423	93	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:89
 aligned with COT1_HUMAN | P10589 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:105
                                    74        84        94       104       114       124       134       144       154       164     
           COT1_HUMAN    65 GTAGDKGQGPPGSGQSQQHIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGRMPPTQPNPG 169
               SCOP domains d2ebla_             A: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......------------............ee..ee.hhhhhhhhhhhhh.......................hhhhhhhhhhhh.hhhhhh..----...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------KR-P------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------NUCLEAR_REC_DBD_2  PDB: A:8-82 UniProt: 83-158                              ----------- PROSITE (1)
                PROSITE (2) ---------------------NUCLEAR_REC_DBD_1          --------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-79 (gaps) UniProt: 1-155 [INCOMPLETE]                                   -------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.4c       Transcript 1 (2)
                 2ebl A   1 GSSGSSG------------IECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRG----SGPSSG  89
                                  |  -         8        18        28        38        48        58        68        78    |   84     
                                  7            8                                                                         83   84

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 '\|'

NMR Structure

Classes(

)

Folds(

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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: automated matches (14)

Protein domain: automated matches (14)

Human (Homo sapiens) [TaxId: 9606] (8)

d2ebla_

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

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

NMR Structure(hide GO term definitions)

Chain A (COT1_HUMAN | P10589)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004879	RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding	Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003707	steroid hormone receptor activity	Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces 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:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	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: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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