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(-) Description

Title :  POLYLYSINE INDUCES AN ANTIPARALLEL ACTIN DIMER THAT NUCLEATES FILAMENT ASSEMBLY: CRYSTAL STRUCTURE AT 3.5 A RESOLUTION
 
Authors :  M. R. Bubb, L. Govindasamy, E. G. Yarmola, S. M. Vorobiev, S. C. Almo, T. Somasundaram, M. S. Chapman, M. Agbandje-Mckenna, R. Mckenna
Date :  06 Apr 02  (Deposition) - 01 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Protein, Muscle Protein, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. R. Bubb, L. Govindasamy, E. G. Yarmola, S. M. Vorobiev, S. C. Almo, T. Somasundaram, M. S. Chapman, M. Agbandje-Mckenna, R. Mckenna
Polylysine Induces An Antiparallel Actin Dimer That Nucleates Filament Assembly: Crystal Structure At 3. 5-A Resolution.
J. Biol. Chem. V. 277 20999 2002
PubMed-ID: 11932258  |  Reference-DOI: 10.1074/JBC.M201371200
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA4Ligand/IonCALCIUM ION
3CL3Ligand/IonCHLORIDE ION
4LAR2Ligand/IonLATRUNCULIN A

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:147 , ASP A:164 , ATP A:390BINDING SITE FOR RESIDUE CA A 412
02AC2SOFTWAREHOH B:5 , HOH B:11 , HOH B:21 , GLN B:1147 , ASP B:1164 , ATP B:1390BINDING SITE FOR RESIDUE CA B 1412
03AC3SOFTWARETYR A:179 , ALA A:180 , GLN B:1364BINDING SITE FOR RESIDUE CA A 503
04AC4SOFTWAREARG A:193 , ARG A:216BINDING SITE FOR RESIDUE CL A 506
05AC5SOFTWAREARG B:1216BINDING SITE FOR RESIDUE CL B 507
06AC6SOFTWAREVAL A:40BINDING SITE FOR RESIDUE CA A 508
07AC7SOFTWAREARG A:157BINDING SITE FOR RESIDUE CL A 512
08AC8SOFTWAREGLY A:23 , SER A:24 , GLY A:25 , LEU A:26 , LYS A:28 , GLY A:166 , ASP A:167 , GLY A:168 , VAL A:169 , LYS A:223 , GLU A:224 , GLY A:312 , THR A:313 , MET A:315 , TYR A:316 , LYS A:346 , LAR A:411 , CA A:412 , HOH A:517 , HOH A:539BINDING SITE FOR RESIDUE ATP A 390
09AC9SOFTWARELEU A:26 , ILE A:44 , GLN A:69 , TYR A:79 , ASP A:167 , GLY A:192 , ARG A:193 , THR A:196 , GLU A:217 , ARG A:220 , LYS A:223 , ATP A:390BINDING SITE FOR RESIDUE LAR A 411
10BC1SOFTWAREHOH B:5 , HOH B:11 , HOH B:21 , GLY B:1023 , SER B:1024 , GLY B:1025 , LEU B:1026 , LYS B:1028 , GLY B:1166 , ASP B:1167 , GLY B:1168 , VAL B:1169 , LYS B:1223 , GLU B:1224 , GLY B:1311 , GLY B:1312 , THR B:1313 , MET B:1315 , LAR B:1411 , CA B:1412BINDING SITE FOR RESIDUE ATP B 1390
11BC2SOFTWAREGLY B:1025 , LEU B:1026 , PRO B:1042 , GLN B:1069 , TYR B:1079 , ASP B:1167 , GLY B:1192 , ARG B:1193 , THR B:1196 , GLU B:1217 , ARG B:1220 , ATP B:1390BINDING SITE FOR RESIDUE LAR B 1411

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:384 -B:1384

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACTINS_1PS00406 Actins signature 1.ACTS_RABIT55-65
 
  2A:63-73
B:1063-1073
2ACTINS_ACT_LIKEPS01132 Actins and actin-related proteins signature.ACTS_RABIT106-118
 
  2A:114-126
B:1114-1126
3ACTINS_2PS00432 Actins signature 2.ACTS_RABIT358-366
 
  2A:366-374
B:1366-1374

(-) Exons   (0, 0)

(no "Exon" information available for 1LCU)

(-) 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:361
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:371
                                    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       376 
          ACTS_RABIT      7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF  377
               SCOP domains d1lcua1 A:15-157 Actin                                                                                                                         d1lcua2 A:158-385 Actin                                                                                                                                                                                                              SCOP domains
               CATH domains -1lcuA01                      1lcuA0          2 A:45-78         --1lcuA01 A:16-44,A:81-144,A:347-379                              -1lcuA03 A:146-191,A:281-342                   1lcuA04 A:192-277 Actin; Chain A, domain 4                                            ---1lcuA03 A:146-191,A:281-342                                   ----1lcuA01                          ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeee.........eeee..ee....----------..eehhhhhhhhhhh.....ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh......................eee.....eee..hhhhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhheeeehhhhhh.hhhhhhhhhhhh.........ee......hhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lcu A   15 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRH----------DSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF  385
                                    24        34        44     |   -      | 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       374       384 
                                                              50         61                                                                                                                                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:371
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:371
                                    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       376 
          ACTS_RABIT      7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF  377
               SCOP domains d1lcub1 B:1015-1157 Actin                                                                                                                      d1lcub2 B:1158-1385 Actin                                                                                                                                                                                                            SCOP domains
               CATH domains 1lcuB01                    1lcuB02 B:1042-1082                      1lcuB01 B:1015-1041,B:1083-1148,B:1348-1384                       1lcuB03 B:1149-1195,B:1285-1347                1lcuB04 B:1196-1284 Actin; Chain A, domain 4                                             1lcuB03 B:1149-1195,B:1285-1347                                1lcuB01                              - CATH domains
           Pfam domains (1) Actin-1lcuB01 B:1015-1385                                                                                                                                                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) Actin-1lcuB02 B:1015-1385                                                                                                                                                                                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author ...eeeee...eeeeee.......eeee..eee...............eehhhhhhhhhhheee..ee..ee.hhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhh.....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhh......ee.......ee..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhh.eeeehhhhhh.hhhhhhhhhhhh.........ee......hhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lcu B 1015 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVVMGQGDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 1385
                                  1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384 

   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  (3, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) 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 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 1yxq 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 1LCU)