1X61 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE FIRST LIM DOMAIN OF THYROID RECEPTOR INTERACTING PROTEIN 6 (TRIP6)

Authors :   X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   17 May 05 (Deposition) - 17 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Lim Domain, Thyroid Receptor Interacting Protein 6 (Trip6), Opa-Interacting Protein 1, Zyxin Related Protein 1 (Zrp-1), Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The First Lim Domain Of Thyroid Receptor Interacting Protein 6 (Trip6)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - THYROID RECEPTOR INTERACTING PROTEIN 6
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040830-09
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIM DOMAIN
	Gene	:	TRIP6, OIP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	TRIP6, OPA-INTERACTING PROTEIN 1, ZYXIN RELATED PROTEIN 1, ZRP-1


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:8 , CYS A:11 , HIS A:30 , CYS A:33	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:36 , CYS A:39 , CYS A:57 , CYS A:60	BINDING SITE FOR RESIDUE ZN A 401

(no "SS Bond" information available for 1X61)

(no "Cis Peptide Bond" information available for 1X61)

NMR Structure (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_050171	V	230	I	TRIP6_HUMAN	Polymorphism	2075756	A	S	2	I
2	UniProt	VAR_013309	L	296	F	TRIP6_HUMAN	Polymorphism	17855370	A	L	25	F

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

NMR Structure (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	TRIP6_HUMAN	279-314 339-372	1	A:8-43 -
2	LIM_DOMAIN_2	PS50023	LIM domain profile.	TRIP6_HUMAN	337-397 277-335 400-467	2	A:66-66 A:8-64 -

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000200457	1a	ENSE00001917757	chr7:100464760-100465228	469	TRIP6_HUMAN	1-37	37	0	-	-
1.2a	ENST00000200457	2a	ENSE00000710158	chr7:100465483-100465610	128	TRIP6_HUMAN	37-79	43	0	-	-
1.2f	ENST00000200457	2f	ENSE00001748387	chr7:100465730-100465855	126	TRIP6_HUMAN	80-121	42	0	-	-
1.3b	ENST00000200457	3b	ENSE00001746150	chr7:100466117-100466488	372	TRIP6_HUMAN	122-245	124	1	A:1-7	7
1.4a	ENST00000200457	4a	ENSE00001633445	chr7:100467992-100468085	94	TRIP6_HUMAN	246-277	32	0	-	-
1.4e	ENST00000200457	4e	ENSE00001701384	chr7:100468196-100468365	170	TRIP6_HUMAN	277-333	57	1	A:8-62	55
1.4i	ENST00000200457	4i	ENSE00001781071	chr7:100469165-100469343	179	TRIP6_HUMAN	334-393	60	1	A:63-72	10
1.5b	ENST00000200457	5b	ENSE00001630795	chr7:100470246-100470366	121	TRIP6_HUMAN	393-433	41	0	-	-
1.6b	ENST00000200457	6b	ENSE00001833240	chr7:100470794-100471076	283	TRIP6_HUMAN	434-476	43	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:72
 aligned with TRIP6_HUMAN | Q15654 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:115
                                   238       248       258       268       278       288       298       308       318       328       338     
          TRIP6_HUMAN   229 GVSGPAGRGRGGEHGPQVPLSQPPEDELDRLTKKLVHDMNHPPSGEYFGQCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLEKCATCS 343
               SCOP domains --------------------------------------------------d1x61a1 A:8-34             d1x61a2 A:35-66                 ------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------LIM-1x61A01 A:8-65                                        ------- Pfam domains
         Sec.struct. author .......-------------------------------------------..............ee....ee..................eee....eeehhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -I-----------------------------------------------------------------F----------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------LIM_DOMAIN_1  PDB: A:8-43           ------------------------LIM_D PROSITE (1)
                PROSITE (2) ------------------------------------------------LIM_DOMAIN_2  PDB: A:8-64 UniProt: 277-335                 -LIM_DOM PROSITE (2)
           Transcript 1 (1) Exon 1.3b        Exon 1.4a  PDB: -               --------------------------------------------------------Exon 1.4i  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.4e  PDB: A:8-62 UniProt: 277-333 [INCOMPLETE]     ---------- Transcript 1 (2)
                 1x61 A   1 GSSGSSG-------------------------------------------CGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLESGPSSG  72
                                  |  -         -         -         -         -|       17        27        37        47        57        67     
                                  7                                           8

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(

)

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: LIM domain (37)

Protein domain: Thyroid receptor interacting protein 6, TRIP6 (2)

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

1a	d1x61a1	A:8-34
1b	d1x61a2	A:35-66

(no "CATH Domain" information available for 1X61)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: LIM] (23)

Family: LIM (23)

Homo sapiens (Human) (18)

LIM-1x61A01

A:8-65

NMR Structure(hide GO term definitions)

Chain A (TRIP6_HUMAN | Q15654)

molecular function
	GO:0005149	interleukin-1 receptor binding	Interacting selectively and non-covalently with the interleukin-1 receptor.
	GO:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0048041	focal adhesion assembly	The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0008588	release of cytoplasmic sequestered NF-kappaB	The release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0045323	interleukin-1 receptor complex	A protein complex that binds interleukin-1; comprises an alpha and a beta subunit.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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	1x61
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