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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE SECOND LIM DOMAIN OF PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN (PINCH)

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

Date :   08 Dec 05 (Deposition) - 08 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Lim Domain; Pinch Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Second Lim Domain Of Particularly Interesting New Cys-His Protein (Pinch)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN PINCH
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050302-42
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIM DOMAIN
	Gene	:	LIMS1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN, LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 1 ,PINCH PROTEIN


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:28 , CYS A:31	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:34 , CYS A:37 , CYS A:55 , CYS A:58	BINDING SITE FOR RESIDUE ZN A 401

(no "SS Bond" information available for 2D8X)

(no "Cis Peptide Bond" information available for 2D8X)

(no "SAP(SNP)/Variant" information available for 2D8X)

NMR Structure (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_2	PS50023	LIM domain profile.	LIMS1_HUMAN	8-69 71-128 191-250 133-190 251-310	2	- A:8-64 - A:70-70 -
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LIMS1_HUMAN	10-45 71-104 135-168 193-226	2	- A:8-41 A:70-70 -

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000393310	3	ENSE00001514785	chr2:109204922-109205084	163	LIMS1_HUMAN	-	0	0	-	-
1.8a	ENST00000393310	8a	ENSE00002191959	chr2:109276061-109276220	160	LIMS1_HUMAN	1-52	52	1	A:1-4	4
1.12a	ENST00000393310	12a	ENSE00001618857	chr2:109287237-109287303	67	LIMS1_HUMAN	53-75	23	1	A:5-12	8
1.14	ENST00000393310	14	ENSE00001746358	chr2:109288781-109288901	121	LIMS1_HUMAN	75-115	41	1	A:12-52	41
1.15a	ENST00000393310	15a	ENSE00002187125	chr2:109289336-109289485	150	LIMS1_HUMAN	115-165	51	1	A:52-70 (gaps)	51
1.16b	ENST00000393310	16b	ENSE00001613279	chr2:109292334-109292484	151	LIMS1_HUMAN	165-215	51	1	A:70-70	1
1.17	ENST00000393310	17	ENSE00001601331	chr2:109293062-109293154	93	LIMS1_HUMAN	216-246	31	0	-	-
1.18	ENST00000393310	18	ENSE00001805893	chr2:109294435-109294483	49	LIMS1_HUMAN	247-263	17	0	-	-
1.19	ENST00000393310	19	ENSE00001629219	chr2:109297151-109297226	76	LIMS1_HUMAN	263-288	26	0	-	-
1.21c	ENST00000393310	21c	ENSE00001514784	chr2:109300341-109303702	3362	LIMS1_HUMAN	288-325	38	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:70
 aligned with LIMS1_HUMAN | P48059 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:141
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164 
          LIMS1_HUMAN    25 NSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKARGLGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCG 165
               SCOP domains ----------------------------------------------d2d8xa2 A:8-32           d2d8xa1 A:33-64                 -------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------------------------------...............eee..eee...................eee..eeehhhhhhhhhh...--------------------------------... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: - UniProt: 8-69           -LIM_DOMAIN_2  PDB: A:8-64 UniProt: 71-128                 ----LIM_DOMAIN_2  PDB: A:70-70        PROSITE (1)
                PROSITE (2) LIM_DOMAIN_1  PDB: - -------------------------LIM_DOMAIN_1  PDB: A:8-41         ------------------------------LIM_DOMAIN_1  PDB: A:70-70      PROSITE (2)
           Transcript 1 (1) Exon 1.8a  PDB: A:1-4       Exon 1.12a  PDB: A:5-12---------------------------------------Exon 1.15a  PDB: A:52-70 (gaps) UniProt: 115-165    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.14  PDB: A:12-52 UniProt: 75-115  -------------------------------------------------1 Transcript 1 (2)
                 2d8x A   1 GSSG---------------------------------------SSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGP--------------------------------SSG  70
                               |     -         -         -         -   |    11        21        31        41        51        61     |   -         -         -        69 
                               4                                       5                                                            67                               68

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(

)

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: Pinch (particularly interesting new Cys-His) protein (5)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d2d8xa1	A:33-64
1b	d2d8xa2	A:8-32

(no "CATH Domain" information available for 2D8X)

(no "Pfam Domain" information available for 2D8X)

NMR Structure(hide GO term definitions)

Chain A (LIMS1_HUMAN | P48059)

molecular function
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007569	cell aging	An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
	GO:0034329	cell junction assembly	A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction.
	GO:0071560	cellular response to transforming growth factor beta stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
	GO:0001837	epithelial to mesenchymal transition	A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
	GO:0045184	establishment of protein localization	The directed movement of a protein to a specific location.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0010811	positive regulation of cell-substrate adhesion	Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
	GO:0051894	positive regulation of focal adhesion assembly	Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1900026	positive regulation of substrate adhesion-dependent cell spreading	Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
	GO:0050678	regulation of epithelial cell proliferation	Any process that modulates the frequency, rate or extent of epithelial cell proliferation.
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:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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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Description

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