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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE LIM DOMAIN OF EPITHELIAL PROTEIN LOST IN NEOPLASM

Authors :   X. R. Qin, T. Nagashima, 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, Epithelial Protein Lost In Neoplasm, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Lim Domain Of Epithelial Protein Lost In Neoplasm
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - EPLIN PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050302-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIM DOMAIN
	Gene	:	EPLIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	EPITHELIAL PROTEIN LOST IN NEOPLASM


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:18 , CYS A:21 , HIS A:39 , CYS A:42	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:45 , CYS A:48 , CYS A:66 , HIS A:69	BINDING SITE FOR RESIDUE ZN A 401

(no "SS Bond" information available for 2D8Y)

(no "Cis Peptide Bond" information available for 2D8Y)

(no "SAP(SNP)/Variant" information available for 2D8Y)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_2	PS50023	LIM domain profile.	LIMA1_HUMAN	388-448	1	A:16-76
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LIMA1_HUMAN	390-424	1	A:18-52

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000341247	1	ENSE00001114650	chr12:50677353-50677203	151	LIMA1_HUMAN	-	0	0	-	-
1.2	ENST00000341247	2	ENSE00001379043	chr12:50642557-50642416	142	LIMA1_HUMAN	1-40	40	0	-	-
1.3	ENST00000341247	3	ENSE00000837648	chr12:50625493-50625448	46	LIMA1_HUMAN	40-55	16	0	-	-
1.5a	ENST00000341247	5a	ENSE00001060480	chr12:50616268-50615804	465	LIMA1_HUMAN	56-210	155	0	-	-
1.6	ENST00000341247	6	ENSE00000424945	chr12:50599851-50599767	85	LIMA1_HUMAN	211-239	29	0	-	-
1.7	ENST00000341247	7	ENSE00000742546	chr12:50598483-50598335	149	LIMA1_HUMAN	239-288	50	0	-	-
1.8	ENST00000341247	8	ENSE00000742547	chr12:50594667-50594560	108	LIMA1_HUMAN	289-324	36	0	-	-
1.9	ENST00000341247	9	ENSE00000742548	chr12:50589670-50589613	58	LIMA1_HUMAN	325-344	20	0	-	-
1.10b	ENST00000341247	10b	ENSE00000919783	chr12:50586344-50586235	110	LIMA1_HUMAN	344-380	37	1	A:1-9	9
1.11	ENST00000341247	11	ENSE00000919782	chr12:50575820-50575687	134	LIMA1_HUMAN	381-425	45	1	A:10-53	44
1.12b	ENST00000341247	12b	ENSE00001666705	chr12:50571852-50569565	2288	LIMA1_HUMAN	425-759	335	1	A:53-91 (gaps)	68

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)
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Chain A from PDB  Type:PROTEIN  Length:91
 aligned with LIMA1_HUMAN | Q9UHB6 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:121
                                   381       391       401       411       421       431       441       451       461       471       481       491 
          LIMA1_HUMAN   372 ESSPPKAMKKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGHRPHKDLWASKNENEEILERPAQLANARETPHSPG 492
               SCOP domains --------d 2d8ya1 A:9-43 Eplin, LIMA1        d2d8ya2 A:44-85 Eplin, LIMA1              ----------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........-....................eee....eee..................ee....eehhhhhhhhh..............-----------------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------LIM_DOMAIN_2  PDB: A:16-76 UniProt: 388-448                  -------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------LIM_DOMAIN_1  PDB: A:18-52         -------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.10b    Exon 1.11  PDB: A:10-53 UniProt: 381-425     ------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.12b  PDB: A:53-91 (gaps) UniProt: 425-759 [INCOMPLETE]        Transcript 1 (2)
                 2d8y A   1 GSSGSSGMK-FQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSGP-----------------------------SSG  91
                                    |-|       19        29        39        49        59        69        79        |-         -         -        90 
                                    9 |                                                                            88                            89  
                                     10

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: Eplin, LIMA1 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2d8ya1	A:9-43
1b	d2d8ya2	A:44-85

(no "CATH Domain" information available for 2D8Y)

(no "Pfam Domain" information available for 2D8Y)

NMR Structure(hide GO term definitions)

Chain A (LIMA1_HUMAN | Q9UHB6)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0003785	actin monomer binding	Interacting selectively and non-covalently with monomeric actin, also known as G-actin.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051017	actin filament bundle assembly	The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
	GO:0030835	negative regulation of actin filament depolymerization	Any process that stops, prevents, or reduces the frequency, rate or extent of actin depolymerization.
	GO:0031529	ruffle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005903	brush border	The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
	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:0032154	cleavage furrow	The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
	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: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.
	GO:0001725	stress fiber	A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

NMR Structure
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Description

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