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(-) Description

Title :  PROFILIN:ACTIN WITH A WIDE OPEN NUCLEOTIDE CLEFT
 
Authors :  J. C. Porta, G. E. Borgstahl
Date :  23 Oct 11  (Deposition) - 25 Apr 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,P
Keywords :  Atpase, Nucleotide Exchange, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Porta, G. E. Borgstahl
Structural Basis For Profilin-Mediated Actin Nucleotide Exchange.
J. Mol. Biol. V. 418 103 2012
PubMed-ID: 22366544  |  Reference-DOI: 10.1016/J.JMB.2012.02.012

(-) Compounds

Molecule 1 - ACTIN, CYTOPLASMIC 1
    Chains: A
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: BETA-ACTIN, ACTIN, CYTOPLASMIC 1, N-TERMINALLY PROCESSED
 
Molecule 2 - PROFILIN-1
    Chains: P
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: PROFILIN I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CA2Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5GOL1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:14 , GLY A:15 , GLY A:156 , ASP A:157 , GLY A:158 , GLY A:182 , ARG A:210 , LYS A:213 , GLU A:214 , GLY A:302 , MET A:305 , TYR A:306 , LYS A:336 , CA A:377 , HOH A:381BINDING SITE FOR RESIDUE ATP A 376
2AC2SOFTWAREGLY A:15 , MET A:16 , ATP A:376BINDING SITE FOR RESIDUE CA A 377
3AC3SOFTWARESER A:199 , THR A:201 , GLU A:205BINDING SITE FOR RESIDUE CA A 378
4AC4SOFTWAREHIS P:133 , ARG P:136BINDING SITE FOR RESIDUE GOL P 140
5AC5SOFTWARETYR P:128 , ALA P:131 , SER P:132 , ARG P:135BINDING SITE FOR RESIDUE CL P 141

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UB5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UB5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UB5)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROFILINPS00414 Profilin signature.PROF1_BOVIN1-9  1P:1-8
2ACTINS_1PS00406 Actins signature 1.ACTB_BOVIN53-63  1A:53-63
3ACTINS_ACT_LIKEPS01132 Actins and actin-related proteins signature.ACTB_BOVIN104-116  1A:104-116
4ACTINS_2PS00432 Actins signature 2.ACTB_BOVIN356-364  1A:356-364

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000064651ENSBTAE00000051693chr19:26821468-26821753286PROF1_BOVIN1-44441P:0-4344
1.2ENSBTAT000000064652ENSBTAE00000051699chr19:26823296-26823488193PROF1_BOVIN45-109651P:44-10865
1.3ENSBTAT000000064653ENSBTAE00000051703chr19:26824096-26824443348PROF1_BOVIN109-140321P:108-13932

(-) 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:370
 aligned with ACTB_BOVIN | P60712 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:370
                                    15        25        35        45        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       375
           ACTB_BOVIN     6 AALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF 375
               SCOP domains d3ub5a1 A:6-146 Actin                                                                                                                        d3ub5a2 A:147-375 Actin                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee........eee..eeee..............eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhh.....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhhhhhhhhh.eehhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ub5 A   6 AALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF 375
                                    15        25        35        45        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       375


Chain P from PDB  Type:PROTEIN  Length:140
 aligned with PROF1_BOVIN | P02584 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          PROF1_BOVIN     1 MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQKCSVIRDSLLQDGEFTMDLRTKSTGGAPTFNITVTMTAKTLVLLMGKEGVHGGMINKKCYEMASHLRRSQY 140
               SCOP domains d3ub5p_ P: Profilin (actin-binding protein)                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...eeeeeeee.....eeeee....hhhhhhhhhhhhhhh...hhhhhhheee..eeeeeeee........eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PROFILIN ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: P:0-43 UniProt: 1-44         Exon 1.2  PDB: P:44-108 UniProt: 45-109                          ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: P:108-139         Transcript 1 (2)
                 3ub5 P   0 xAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQKCSVIRDSLLQDGEFTMDLRTKSTGGAPTFNITVTMTAKTLVLLMGKEGVHGGMINKKCYEMASHLRRSQY 139
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139
                            0-ACE
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UB5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UB5)

(-) Gene Ontology  (16, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACTB_BOVIN | P60712)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0051086    chaperone mediated protein folding independent of cofactor    The process of assisting in the correct noncovalent assembly of posttranslational proteins and does not depend on additional protein cofactors. This function occurs over one or more cycles of nucleotide-dependent binding and release.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
cellular component
    GO:0035267    NuA4 histone acetyltransferase complex    A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0097433    dense body    An electron dense body which may contain granules.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain P   (PROF1_BOVIN | P02584)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
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:0032233    positive regulation of actin filament bundle assembly    Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0030833    regulation of actin filament polymerization    Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACTB_BOVIN | P60712: 1hlu 2btf 2oan 3u4l
        PROF1_BOVIN | P02584: 1hlu 1pne 2btf 3u4l

(-) Related Entries Specified in the PDB File

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