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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF THE HUMAN ALPHA-ACTININ ISOFORM 3
 
Authors :  G. Franzot, B. Sjoblom, M. Gautel, K. Djinovic Carugo
Date :  08 Jun 04  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Calponin Homology Domain, Actin Binding Domain, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Franzot, B. Sjoblom, M. Gautel, K. Djinovic Carugo
The Crystal Structure Of The Actin Binding Domain From Alpha-Actinin In Its Closed Conformation: Structural Insight Into Phospholipid Regulation Of Alpha-Actinin
J. Mol. Biol. V. 348 151 2005
PubMed-ID: 15808860  |  Reference-DOI: 10.1016/J.JMB.2005.01.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-ACTININ 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System StrainBL21[DE3]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentACTIN BINDING DOMAIN (ABD)
    GeneACTN3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA ACTININ SKELETAL MUSCLE ISOFORM 3, F-ACTIN CROSS LINKING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WKU)

(-) Sites  (0, 0)

(no "Site" information available for 1WKU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 8)

Asymmetric Unit (3, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.ACTN3_HUMAN45-149
 
158-261
 
  4A:45-149
B:45-149
A:158-261
B:158-261
2ACTININ_1PS00019 Actinin-type actin-binding domain signature 1.ACTN3_HUMAN47-56
 
  2A:47-56
B:47-56
3ACTININ_2PS00020 Actinin-type actin-binding domain signature 2.ACTN3_HUMAN121-145
 
  2A:121-145
B:121-145
Biological Unit 1 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.ACTN3_HUMAN45-149
 
158-261
 
  2A:45-149
-
A:158-261
-
2ACTININ_1PS00019 Actinin-type actin-binding domain signature 1.ACTN3_HUMAN47-56
 
  1A:47-56
-
3ACTININ_2PS00020 Actinin-type actin-binding domain signature 2.ACTN3_HUMAN121-145
 
  1A:121-145
-
Biological Unit 2 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.ACTN3_HUMAN45-149
 
158-261
 
  2-
B:45-149
-
B:158-261
2ACTININ_1PS00019 Actinin-type actin-binding domain signature 1.ACTN3_HUMAN47-56
 
  1-
B:47-56
3ACTININ_2PS00020 Actinin-type actin-binding domain signature 2.ACTN3_HUMAN121-145
 
  1-
B:121-145

(-) Exons   (0, 0)

(no "Exon" information available for 1WKU)

(-) Sequences/Alignments

Asymmetric Unit
   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:225
 aligned with ACTN3_HUMAN | Q08043 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:225
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
          ACTN3_HUMAN    42 AWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQNFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDIVNTPKPDEKAIMTYVSCFYHAFAGA 266
               SCOP domains d1wkua1 A:42-155 automated matches                                                                                d1wkua2 A:156-266 automated matches                                                                             SCOP domains
               CATH domains 1wkuA01 A:42-153 Actin-binding Protein, T-fimbrin; domain 1                                                     1wkuA02 A:154-266 Actin-binding Protein, T-fimbrin; domain 1                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhh..........hhhhh.hhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CH  PDB: A:45-149 UniProt: 45-149                                                                        --------CH  PDB: A:158-261 UniProt: 158-261                                                                     ----- PROSITE (1)
                PROSITE (2) -----ACTININ_1 ----------------------------------------------------------------ACTININ_2  PDB: A:121-145------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wku A  42 AWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQNFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDIVNTPKPDEKAIMTYVSCFYHAFAGA 266
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with ACTN3_HUMAN | Q08043 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:227
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
          ACTN3_HUMAN    42 AWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQNFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDIVNTPKPDEKAIMTYVSCFYHAFAGAEQ 268
               SCOP domains d1wkub1 B:42-155 automated matches                                                                                d1wkub2 B:156-268 automated matches                                                                               SCOP domains
               CATH domains 1wkuB01 B:42-153 Actin-binding Protein, T-fimbrin; domain 1                                                     1wkuB02 B:154-268 Actin-binding Protein, T-fimbrin; domain 1                                                        CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------CH-1wkuB01 B:161-264                                                                                    ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------CH-1wkuB02 B:161-264                                                                                    ---- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------CH-1wkuB03 B:161-264                                                                                    ---- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------CH-1wkuB04 B:161-264                                                                                    ---- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh........hhhhhhh.hhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhh..........hhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CH  PDB: B:45-149 UniProt: 45-149                                                                        --------CH  PDB: B:158-261 UniProt: 158-261                                                                     ------- PROSITE (1)
                PROSITE (2) -----ACTININ_1 ----------------------------------------------------------------ACTININ_2  PDB: B:121-145--------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wku B  42 AWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQNFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDIVNTPKPDEKAIMTYVSCFYHAFAGAEQ 268
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: CH (43)
(-)
Family: CH (43)
1aCH-1wkuB01B:161-264
1bCH-1wkuB02B:161-264
1cCH-1wkuB03B:161-264
1dCH-1wkuB04B:161-264

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACTN3_HUMAN | Q08043)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008307    structural constituent of muscle    The action of a molecule that contributes to the structural integrity of a muscle fiber.
biological process
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0030049    muscle filament sliding    The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
    GO:0070885    negative regulation of calcineurin-NFAT signaling cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the calcineurin-NFAT signaling cascade.
    GO:0045820    negative regulation of glycolytic process    Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
    GO:0090324    negative regulation of oxidative phosphorylation    Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
    GO:1904025    positive regulation of glucose catabolic process to lactate via pyruvate    Any process that activates or increases the frequency, rate or extent of glucose catabolic process to lactate via pyruvate.
    GO:0048633    positive regulation of skeletal muscle tissue growth    Any process that activates, maintains or increases the rate of skeletal muscle growth.
    GO:1903715    regulation of aerobic respiration    Any process that modulates the frequency, rate or extent of aerobic respiration.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0014728    regulation of the force of skeletal muscle contraction    Any process that modulates the frequency, rate or extent of the force of skeletal muscle contraction. The force of skeletal muscle contraction is produced by acto-myosin interaction processes through the formation of cross bridges.
    GO:0014894    response to denervation involved in regulation of muscle adaptation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a denervation stimulus. This process occurs as part of the regulation of muscle adaptation.
    GO:0014732    skeletal muscle atrophy    A process, occurring in skeletal muscle, that is characterized by a decrease in protein content, fiber diameter, force production and fatigue resistance in response to different conditions such as starvation, aging and disuse.
    GO:0014883    transition between fast and slow fiber    The process of conversion of fast-contracting muscle fibers to a slower character. This may involve slowing of contractile rate, slow myosin gene induction, increase in oxidative metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
cellular component
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0031143    pseudopodium    A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ACTN3_HUMAN | Q080431tjt 3lue

(-) Related Entries Specified in the PDB File

1aoa FIMBRIN
1dxx DYSTROPHIN
1mb8 PLECTIN
1qag UTROPHIN
1tjt THE SAME PROTEIN AT 2.2 ANGSTROM