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Description

Title :   SOLUTION STRUCTURE OF THE LIM DOMAIN OF THE HUMAN ACTIN BINDING LIM PROTEIN 2

Authors :   K. Miyamoto, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   29 Nov 03 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Lim Domain, Zinc Binding Domain, Actin Binding Lim Protein 2, Ablim2, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Miyamoto, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Lim Domain Of The Human Actin Binding Lim Protein 2
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - ACTIN BINDING LIM PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P020930-36
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIM DOMAIN
	Gene	:	KAZUSA CDNA FK00917
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	KIAA1808 PROTEIN

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:38 , CYS A:41	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:44 , CYS A:47 , CYS A:66 , CYS A:69	BINDING SITE FOR RESIDUE ZN A 401

SS Bonds (0, 0)

(no "SS Bond" information available for 1V6G)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1V6G)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1V6G)

PROSITE Motifs (2, 2)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_2	PS50023	LIM domain profile.	ABLM2_HUMAN	22-81 82-141 151-210 211-270	1	- A:17-75 - -
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	ABLM2_HUMAN	24-57 83-116 153-187 212-245	1	- A:18-51 - -

Exons (2, 2)

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000341937	1d	ENSE00002025557	chr4:8160481-8160407	75	ABLM2_HUMAN	1-4	4	0	-	-
1.2	ENST00000341937	2	ENSE00001798266	chr4:8108364-8108221	144	ABLM2_HUMAN	4-52	49	0	-	-
1.3	ENST00000341937	3	ENSE00001651357	chr4:8099009-8098826	184	ABLM2_HUMAN	52-113	62	1	A:1-48 (gaps)	60
1.4	ENST00000341937	4	ENSE00001645970	chr4:8090011-8089896	116	ABLM2_HUMAN	113-152	40	1	A:48-81 (gaps)	37
1.5	ENST00000341937	5	ENSE00001741599	chr4:8082529-8082403	127	ABLM2_HUMAN	152-194	43	0	-	-
1.6	ENST00000341937	6	ENSE00001673927	chr4:8079448-8079355	94	ABLM2_HUMAN	194-225	32	0	-	-
1.8	ENST00000341937	8	ENSE00001735996	chr4:8062781-8062694	88	ABLM2_HUMAN	226-255	30	0	-	-
1.9	ENST00000341937	9	ENSE00001080335	chr4:8055973-8055915	59	ABLM2_HUMAN	255-274	20	0	-	-
1.10	ENST00000341937	10	ENSE00001080338	chr4:8046968-8046891	78	ABLM2_HUMAN	275-300	26	0	-	-
1.12	ENST00000341937	12	ENSE00001080331	chr4:8038022-8037876	147	ABLM2_HUMAN	301-349	49	0	-	-
1.14	ENST00000341937	14	ENSE00001080332	chr4:8031503-8031383	121	ABLM2_HUMAN	350-390	41	0	-	-
1.16d	ENST00000341937	16d	ENSE00001337667	chr4:8022030-8021929	102	ABLM2_HUMAN	390-424	35	0	-	-
1.17	ENST00000341937	17	ENSE00001136408	chr4:8021398-8021345	54	ABLM2_HUMAN	424-442	19	0	-	-
1.19	ENST00000341937	19	ENSE00001136400	chr4:8010829-8010777	53	ABLM2_HUMAN	442-459	18	0	-	-
1.20e	ENST00000341937	20e	ENSE00001492451	chr4:8009924-8009786	139	ABLM2_HUMAN	460-506	47	0	-	-
1.21	ENST00000341937	21	ENSE00001278544	chr4:7994654-7994593	62	ABLM2_HUMAN	506-526	21	0	-	-
1.22	ENST00000341937	22	ENSE00001278537	chr4:7986620-7986566	55	ABLM2_HUMAN	527-545	19	0	-	-
1.23	ENST00000341937	23	ENSE00001772276	chr4:7985281-7985274	8	ABLM2_HUMAN	545-547	3	0	-	-
1.24b	ENST00000341937	24b	ENSE00001278486	chr4:7985071-7984991	81	ABLM2_HUMAN	548-574	27	0	-	-
1.25c	ENST00000341937	25c	ENSE00002068146	chr4:7968830-7968029	802	ABLM2_HUMAN	575-611	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
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Chain A from PDB  Type:PROTEIN  Length:81
 aligned with ABLM2_HUMAN | Q6H8Q1 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:96
                                    63        73        83        93       103       113       123       133       143      
          ABLM2_HUMAN    54 GCDLAEGGFFVRQGEYICTLDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVGSSAHLSQG 149
               SCOP domains d1v6ga1             A:1-41                           d1v6ga2 A:42-81                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------LIM-1v6gA01 A:18-72                                    ------------ Pfam domains (1)
           Pfam domains (2) -----------------------------LIM-1v6gA02 A:18-72                                    ------------ Pfam domains (2)
         Sec.struct. author .......------------..hhh.................eee..eee...................eeee..eeeehhhh........---... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: -        LIM_DOMAIN_2  PDB: A:17-75 UniProt: 82-141                  -------- PROSITE (1)
                PROSITE (2) LIM_-------------------------LIM_DOMAIN_1  PDB: A:18-51        --------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:1-48 (gaps) UniProt: 52-113 [INCOMPLETE]   ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4  PDB: A:48-81 (gaps)         Transcript 1 (2)
                 1v6g A   1 GSSGSSG------------LDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVSGP---SSG  81
                                  |  -         8        18        28        38        48        58        68        78   |  
                                  7            8                                                                    78  79

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 '\|'

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 2, abLIM2 (2)

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

1a	d1v6ga1	A:1-41
1b	d1v6ga2	A:42-81

CATH Domains (0, 0)

(no "CATH Domain" information available for 1V6G)

Pfam Domains (1, 2)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: LIM (23)

Homo sapiens (Human) (18)

1a	LIM-1v6gA01	A:18-72
1b	LIM-1v6gA02	A:18-72

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (ABLM2_HUMAN | Q6H8Q1)

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: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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	ABLM2_HUMAN \| Q6H8Q1	:	1wig 2l3x

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