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Description

Title :   SOLUTION STRUCTURE OF 3RD LIM DOMAIN OF ACTIN-BINDING LIM PROTEIN 3

Authors :   T. N. Niraula, A. Sasagawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   31 Mar 06 (Deposition) - 01 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Lim Domain, Actin-Binding Lim Protein 3, Zn Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. N. Niraula, A. Sasagawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of 3Rd Lim Domain Of Actin-Binding Lim Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - ACTIN-BINDING LIM PROTEIN 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050111-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIM DOMAIN
	Gene	:	ABLIM3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	ACTIN-BINDING LIM PROTEIN FAMILY MEMBER 3, ABLIM3

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

NMR Structure (1, 2)

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

Sites (2, 2)

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:65 , ASP A:68	BINDING SITE FOR RESIDUE ZN A 401

SS Bonds (0, 0)

(no "SS Bond" information available for 2DJ7)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2DJ7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_050143	G	125	D	ABLM3_HUMAN	Polymorphism	35907283	A	G	4	D

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

PROSITE Motifs (2, 3)

NMR Structure (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_2	PS50023	LIM domain profile.	ABLM3_HUMAN	21-80 81-140 149-208 209-268	2	- - A:16-74 A:75-77
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	ABLM3_HUMAN	23-56 82-115 151-185 210-243	2	- - A:18-52 A:75-77

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000309868	1c	ENSE00001878782	chr5:148521066-148521217	152	ABLM3_HUMAN	-	0	0	-	-
1.1g	ENST00000309868	1g	ENSE00001427228	chr5:148521572-148521671	100	ABLM3_HUMAN	1-5	5	0	-	-
1.2a	ENST00000309868	2a	ENSE00001201072	chr5:148563015-148563152	138	ABLM3_HUMAN	5-51	47	0	-	-
1.3	ENST00000309868	3	ENSE00001201051	chr5:148577782-148577965	184	ABLM3_HUMAN	51-112	62	0	-	-
1.5a	ENST00000309868	5a	ENSE00001201047	chr5:148579879-148579991	113	ABLM3_HUMAN	112-150	39	1	A:1-17 (gaps)	33
1.6	ENST00000309868	6	ENSE00001201038	chr5:148586571-148586697	127	ABLM3_HUMAN	150-192	43	1	A:17-59	43
1.7	ENST00000309868	7	ENSE00001201031	chr5:148590289-148590382	94	ABLM3_HUMAN	192-223	32	1	A:59-76 (gaps)	28
1.8	ENST00000309868	8	ENSE00001201023	chr5:148596522-148596609	88	ABLM3_HUMAN	224-253	30	1	A:77-80	4
1.9	ENST00000309868	9	ENSE00001201016	chr5:148610212-148610270	59	ABLM3_HUMAN	253-272	20	0	-	-
1.10a	ENST00000309868	10a	ENSE00001201012	chr5:148612792-148612863	72	ABLM3_HUMAN	273-296	24	0	-	-
1.11	ENST00000309868	11	ENSE00001201007	chr5:148617011-148617166	156	ABLM3_HUMAN	297-348	52	0	-	-
1.12	ENST00000309868	12	ENSE00001269114	chr5:148618811-148618840	30	ABLM3_HUMAN	349-358	10	0	-	-
1.13	ENST00000309868	13	ENSE00001201000	chr5:148619322-148619451	130	ABLM3_HUMAN	359-402	44	0	-	-
1.15	ENST00000309868	15	ENSE00001200997	chr5:148620239-148620337	99	ABLM3_HUMAN	402-435	34	0	-	-
1.16a	ENST00000309868	16a	ENSE00001200993	chr5:148622054-148622101	48	ABLM3_HUMAN	435-451	17	0	-	-
1.17b	ENST00000309868	17b	ENSE00001200990	chr5:148624444-148624578	135	ABLM3_HUMAN	451-496	46	0	-	-
1.18	ENST00000309868	18	ENSE00001200988	chr5:148626045-148626109	65	ABLM3_HUMAN	496-517	22	0	-	-
1.19	ENST00000309868	19	ENSE00001200983	chr5:148627345-148627492	148	ABLM3_HUMAN	518-567	50	0	-	-
1.20	ENST00000309868	20	ENSE00001269072	chr5:148629378-148629407	30	ABLM3_HUMAN	567-577	11	0	-	-
1.21	ENST00000309868	21	ENSE00001200975	chr5:148630010-148630068	59	ABLM3_HUMAN	577-596	20	0	-	-
1.22	ENST00000309868	22	ENSE00001200967	chr5:148630922-148630982	61	ABLM3_HUMAN	597-617	21	0	-	-
1.23	ENST00000309868	23	ENSE00001689480	chr5:148631764-148631771	8	ABLM3_HUMAN	617-619	3	0	-	-
1.24b	ENST00000309868	24b	ENSE00001200957	chr5:148632320-148632400	81	ABLM3_HUMAN	620-646	27	0	-	-
1.25d	ENST00000309868	25d	ENSE00001890112	chr5:148637854-148640002	2149	ABLM3_HUMAN	647-683	37	0	-	-

Sequences/Alignments

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:80
 aligned with ABLM3_HUMAN | O94929 from UniProtKB/Swiss-Prot  Length:683

    Alignment length:117
                                   127       137       147       157       167       177       187       197       207       217       227       
          ABLM3_HUMAN   118 GDKVTFSGKECVCQTCSQSMASSKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYHAQFGIKCETCDRYISGRVLEAGGKHYHPTCA 234
               SCOP domains -----------------------d2dj7a2 A:8-43                      d2dj7a1 A:44-74                --------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----..------------..........................eee..eee..................eee..eee..hhhhhhh.----------..-----------.... Sec.struct. author
                 SAPs(SNPs) -------D------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: -   --------LIM_DOMAIN_2  PDB: A:16-74 UniProt: 149-208                 LIM_DOMAIN_2  PDB: A:75-77 PROSITE (1)
                PROSITE (2) ---------------------------------LIM_DOMAIN_1  PDB: A:18-52         ------------------------LIM_DOMAIN_1  PDB: A:75-7 PROSITE (2)
           Transcript 1 (1) Exon 1.5a  PDB: A:1-17 (gaps)    -----------------------------------------Exon 1.7  PDB: A:59-76 (gaps)   Exon 1.8    Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.6  PDB: A:17-59 UniProt: 150-192    ------------------------------------------ Transcript 1 (2)
                 2dj7 A   1 GS----SG------------SSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYHAQFG----------SG-----------PSSG  80
                             |    || -         -|       14        24        34        44        54        64        74         -||       -   |   
                             2    3|            5                                                                   74         75|          77   
                                   4                                                                                            76

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

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: Actin-binding LIM protein 3, abLIM-3 (1)

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

1a	d2dj7a1	A:44-74
1b	d2dj7a2	A:8-43

CATH Domains (0, 0)

(no "CATH Domain" information available for 2DJ7)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2DJ7)

Gene Ontology (13, 13)

NMR Structure(hide GO term definitions)

Chain A (ABLM3_HUMAN | O94929)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	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:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0030032	lamellipodium assembly	Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	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.

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Related Entries

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	ABLM3_HUMAN \| O94929	:	1ujs

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