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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST LIM DOMAIN FROM HUMAN FOUR AND A HALF LIM DOMAINS PROTEIN 3
 
Authors :  K. Inoue, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Mar 07  (Deposition) - 11 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lim Domain, Four And A Half Lim Domains Protein 3, Fhl-3, Skeletal Muscle Lim- Protein 2, Slim 2, Fhl3, Slim2, 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 :  K. Inoue, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The First Lim Domain From Human Four And A Half Lim Domains Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FOUR AND A HALF LIM DOMAINS 3
    Chains: A
    Engineered: YES
    Expression System Plasmid: P060911-22
    Expression System Vector Type: PLASMID
    Fragment: LIM DOMAIN
    Gene: FHL3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: FHL-3, SKELETAL MUSCLE LIM- PROTEIN 2, SLIM 2

 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.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:18 , CYS A:21 , HIS A:40 , CYS A:43BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARECYS A:46 , CYS A:49 , CYS A:67 , CYS A:70BINDING SITE FOR RESIDUE ZN A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.FHL3_HUMAN40-75
101-136
162-195
221-258		  2A:18-53
A:77-78
-
-
2LIM_DOMAIN_2PS50023 LIM domain profile.FHL3_HUMAN99-160
38-98
219-280
161-218		  2A:77-82
A:16-76
-
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003730161bENSE00001917363chr1:38471177-38471029149FHL3_HUMAN-00--
1.2ENST000003730162ENSE00002160660chr1:38465104-38464929176FHL3_HUMAN1-52521A:1-30 (gaps)37
1.3aENST000003730163aENSE00001319279chr1:38464820-38464646175FHL3_HUMAN53-111591A:31-7646
1.4ENST000003730164ENSE00001302258chr1:38463804-38463635170FHL3_HUMAN111-167571A:77-82 (gaps)17
1.5ENST000003730165ENSE00001296101chr1:38463542-38463356187FHL3_HUMAN168-230630--
1.6cENST000003730166cENSE00001833847chr1:38463231-38462442790FHL3_HUMAN230-280510--

(-) 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:82
 aligned with FHL3_HUMAN | Q13643 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:131
                                    25        35        45        55        65        75        85        95       105       115       125       135       145 
           FHL3_HUMAN    16 GRKYIQTDSGPYCVPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSQCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKG 146
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---.....----..................................................eeee..eeee......hhh-------------------------------hh-----------.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------LIM_DOMAIN_1  PDB: A:18-53          -------------------------LIM_DOMAIN_1  PDB: A:77-78          ---------- PROSITE (1)
                PROSITE (2) ----------------------LIM_DOMAIN_2  PDB: A:16-76 UniProt: 38-98                    LIM_DOMAIN_2  PDB: A:77-82 UniProt: 99-160       PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:1-30 (gaps)         Exon 1.3a  PDB: A:31-76 UniProt: 53-111 [INCOMPLETE]       ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.4  PDB: A:77-82 (gaps)        Transcript 1 (2)
                 2ehe A   1 GS---SGSSG----PCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS-------------------------------SG-----------PSSG  82
                             |   |   7    |   13        23        33        43        53        63        73  |      -         -         -    ||   -       |81 
                             2   3   7    8                                                                  76                              77|          79   
                                                                                                                                              78
   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  (0, 0)

(no "SCOP Domain" information available for 2EHE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (FHL3_HUMAN | Q13643)
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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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: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: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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UniProtKB/Swiss-Prot
        FHL3_HUMAN | Q13643: 1wyh 2cuq

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