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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIN IN COMPLEX WITH SWINHOLIDE A
 
Authors :  V. A. Klenchin, R. King, J. Tanaka, G. Marriott, I. Rayment
Date :  22 Feb 05  (Deposition) - 17 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Actin; Swinholide A; Macrolide Toxin, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. A. Klenchin, R. King, J. Tanaka, G. Marriott, I. Rayment
Structural Basis Of Swinholide A Binding To Actin
Chem. Biol. V. 12 287 2005
PubMed-ID: 15797212  |  Reference-DOI: 10.1016/J.CHEMBIOL.2005.02.011

(-) Compounds

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
    ChainsA, B
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymALPHA-ACTIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3HIC2Mod. Amino Acid4-METHYL-HISTIDINE
4MG3Ligand/IonMAGNESIUM ION
5SWI1Ligand/IonSWINHOLIDE A

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREATP A:1380 , HOH A:9002 , HOH A:9003 , HOH A:9004 , HOH A:9005BINDING SITE FOR RESIDUE MG A 1390
2AC2SOFTWAREATP B:2380 , HOH B:9003 , HOH B:9004 , HOH B:9005 , HOH B:9006BINDING SITE FOR RESIDUE MG B 2390
3AC3SOFTWAREGLU A:205 , HOH A:9006 , HOH A:9007 , HOH A:9008 , HOH A:9009 , HOH A:9010BINDING SITE FOR RESIDUE MG A 5001
4AC4SOFTWAREGLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:156 , ASP A:157 , GLY A:182 , ARG A:183 , ARG A:210 , LYS A:213 , GLU A:214 , GLY A:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , LYS A:336 , MG A:1390 , HOH A:9003 , HOH A:9004 , HOH A:9005 , HOH A:9064 , HOH A:9083 , HOH A:9089 , HOH A:9098 , HOH A:9169 , HOH A:9175 , HOH A:9190BINDING SITE FOR RESIDUE ATP A 1380
5AC5SOFTWAREGLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLY B:156 , ASP B:157 , GLY B:158 , VAL B:159 , GLY B:182 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , THR B:303 , MET B:305 , TYR B:306 , MG B:2390 , HOH B:9003 , HOH B:9004 , HOH B:9005 , HOH B:9006BINDING SITE FOR RESIDUE ATP B 2380
6AC6SOFTWAREASP A:24 , ASP A:25 , TYR A:143 , ALA A:144 , SER A:145 , GLY A:146 , TYR A:169 , SER A:344 , ILE A:345 , SER A:348 , LEU A:349 , THR A:351 , MET A:355 , HOH A:9224 , GLY B:23 , ASP B:24 , TYR B:133 , TYR B:143 , ALA B:144 , SER B:145 , GLY B:146 , ARG B:147 , ILE B:341 , SER B:344 , SER B:348 , LEU B:349 , THR B:351 , MET B:355 , HOH B:9011 , HOH B:9013 , HOH B:9027 , HOH B:9033 , HOH B:9036BINDING SITE FOR RESIDUE SWI B 600
7AC7SOFTWAREALA A:144 , SER A:145 , PRO A:332 , GLU A:334 , ILE A:341 , HOH A:9176 , HOH A:9222BINDING SITE FOR RESIDUE EDO A 9001
8AC8SOFTWAREALA B:144 , PRO B:332BINDING SITE FOR RESIDUE EDO B 9002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACTINS_1PS00406 Actins signature 1.ACTS_RABIT55-65
 
  2A:53-63
B:53-63
2ACTINS_ACT_LIKEPS01132 Actins and actin-related proteins signature.ACTS_RABIT106-118
 
  2A:104-116
B:104-116
3ACTINS_2PS00432 Actins signature 2.ACTS_RABIT358-366
 
  2A:356-364
B:356-364

(-) Exons   (0, 0)

(no "Exon" information available for 1YXQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:356
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:367
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       
           ACTS_RABIT     7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVH 373
               SCOP domains d1yxqa1 A:5-146 Actin                                                                                                                         d1yxqa2 A:147-371 Actin                                                                                                                                                                                                           SCOP domains
               CATH domains 1yxqA01 A:5-137,A:339-371  [code=3.           30.420.40, no name defined]                                                            1yxqA02 A:138-179,A:272-338               1yxqA03 A:180-271 Actin; Chain A, domain 4                                                  1yxqA02 A:138-179,A:272-338  [code=3.30.420.40, no name defined]   1yxqA01 A:5-137,A:339-371         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..eeee.-----------..eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yxq A   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPR-----------DSYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVH 371
                                    14        24        34    |    -      | 54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       
                                                             39          51                    73-HIC                                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:369
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367         
           ACTS_RABIT     8 TALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKC 376
               SCOP domains d1yxqb1 B:6-146 Actin                                                                                                                        d1yxqb2 B:147-374 Actin                                                                                                                                                                                                              SCOP domains
               CATH domains 1yxqB01 B:6-137,B:339-374  [code=3.          30.420.40, no name defined]                                                            1yxqB02 B:138-179,B:272-338               1yxqB03 B:180-271 Actin; Chain A, domain 4                                                  1yxqB02 B:138-179,B:272-338  [code=3.30.420.40, no name defined]   1yxqB01 B:6-137,B:339-374            CATH domains
           Pfam domains (1) Actin-1yxqB01 B:6-374                                                                                                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Actin-1yxqB02 B:6-374                                                                                                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeee...eeeeee.......eeee..eeee..----------..eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhh......eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhheehhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ---------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yxq B   6 TALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRH----------DSYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKC 374
                                    15        25        35    |    -     |  55        65       |75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365         
                                                             40         51                    73-HIC                                                                                                                                                                                                                                                                                                         

   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/Biological Unit

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ACTS_RABIT | P68135)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
biological process
    GO:0090131    mesenchyme migration    The process in which the population of cells that make up a mesenchyme undergo directed movement.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0048741    skeletal muscle fiber development    The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0030240    skeletal muscle thin filament assembly    The aggregation, arrangement and bonding together of proteins to form the actin-based thin filaments of myofibrils in skeletal muscle.
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:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    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.
    GO:0005865    striated muscle thin filament    Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACTS_RABIT | P681351alm 1atn 1eqy 1esv 1h1v 1ijj 1j6z 1kxp 1lcu 1lot 1m8q 1ma9 1mvw 1nwk 1o18 1o19 1o1a 1o1b 1o1c 1o1d 1o1e 1o1f 1o1g 1p8z 1qz5 1qz6 1rdw 1rfq 1rgi 1s22 1sqk 1t44 1uy5 1wua 1y64 2a3z 2a40 2a41 2a42 2a5x 2asm 2aso 2asp 2d1k 2ff3 2ff6 2fxu 2gwj 2gwk 2hmp 2pav 2pbd 2q0r 2q0u 2q1n 2q31 2q36 2q97 2v51 2v52 2vcp 2vyp 2w49 2w4u 2y83 2yje 2yjf 2zwh 3b5u 3buz 3cjb 3cjc 3daw 3ffk 3g37 3hbt 3j4k 3j8a 3j8i 3j8j 3j8k 3jbi 3jbj 3jbk 3m1f 3m3n 3m6g 3mfp 3mn5 3sjh 3tpq 3tu5 3u8x 3u9z 3ue5 4a7f 4a7h 4a7l 4a7n 4b1v 4b1w 4b1x 4b1y 4b1z 4eah 4gy2 4h03 4h0t 4h0v 4h0x 4h0y 4k41 4k42 4k43 4pkg 4pkh 4pki 4pl8 4v0u 4wyb 4z94 5h53 5jlf 5kg8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YXQ)