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(-) Description

Title :  CRYSTAL STRUCTURE OF A FILAMENT-LIKE ACTIN TRIMER BOUND TO THE BACTERIAL EFFECTOR VOPL
 
Authors :  D. R. Tomchick, J. A. Zahm, M. K. Rosen
Date :  08 Aug 13  (Deposition) - 23 Oct 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Actin Nucleator, Actin Nucleation, Hydrolase, Wasp Homology 2 Domain, Vopl C-Terminal Domain, Cytoskeleton, Atp-Binding Protein, Actin- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Zahm, S. B. Padrick, Z. Chen, C. W. Pak, A. A. Yunus, L. Henry, D. R. Tomchick, Z. Chen, M. K. Rosen
The Bacterial Effector Vopl Organizes Actin Into Filament-Like Structures.
Cell(Cambridge, Mass. ) V. 155 423 2013
PubMed-ID: 24120140  |  Reference-DOI: 10.1016/J.CELL.2013.09.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - T3SS2 EFFECTOR VOPL NUCLEATION OF ACTIN POLYMERIZATION
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: BL21(DE3)T1R
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VOPL C-TERMINAL DOMAIN RESIDUES 247-484
    Gene: VOPL, VPBB_A1249
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 1211705
    Strain: BB22OP
 
Molecule 2 - ACTIN-5C
    Chains: C, D, E
    EC Number: 3.6.1.3
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector: P-FASTBAC
    Expression System Vector Type: BACULOVIRUS
    Gene: 5C-ACTIN, ACT5C, CG4027
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA3Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:13 , SER C:14 , GLY C:15 , MET C:16 , LYS C:18 , GLY C:156 , ASP C:157 , GLY C:158 , VAL C:159 , GLY C:182 , LYS C:213 , GLU C:214 , GLY C:302 , THR C:303 , MET C:305 , TYR C:306 , LYS C:336 , CA C:402BINDING SITE FOR RESIDUE ATP C 401
2AC2SOFTWAREATP C:401BINDING SITE FOR RESIDUE CA C 402
3AC3SOFTWAREGLY D:13 , SER D:14 , GLY D:15 , MET D:16 , LYS D:18 , GLY D:156 , ASP D:157 , GLY D:158 , VAL D:159 , ARG D:210 , LYS D:213 , GLU D:214 , GLY D:301 , GLY D:302 , THR D:303 , MET D:305 , TYR D:306 , LYS D:336 , CA D:402BINDING SITE FOR RESIDUE ATP D 401
4AC4SOFTWAREATP D:401BINDING SITE FOR RESIDUE CA D 402
5AC5SOFTWAREGLY E:13 , SER E:14 , GLY E:15 , MET E:16 , LYS E:18 , GLN E:137 , GLY E:156 , ASP E:157 , VAL E:159 , GLY E:182 , LYS E:213 , GLU E:214 , GLY E:301 , GLY E:302 , THR E:303 , MET E:305 , LYS E:336 , CA E:402BINDING SITE FOR RESIDUE ATP E 401
6AC6SOFTWAREASP E:11 , GLN E:137 , ATP E:401BINDING SITE FOR RESIDUE CA E 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M63)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M63)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M63)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M63)

(-) Exons   (0, 0)

(no "Exon" information available for 4M63)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhh..hhhhhhhhhhhh.hhhhh....ee.......hhhhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m63 A 247 RLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEMAKSEHRYVQAFCREILKYPDCYKSADVASPESPKSVIDVALKRLQTGRERLFTTTDEKGNRELKKGDAILESAINAARMAISTEEKNTILSNNVKSATFDVFCELPCMDGFAEQNGKTAFYALRAGFYSAFKNTDTAKQDITKFMKDNLQAGFSGYSYQGLTNRVAQLEA 474
                                   256       266       276       286       296       306       316       326       340       350       360       370       380       390       400       410       420       430       440       450       460       470    
                                                                                                                 334|                                                                                                                                       
                                                                                                                  339                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhh...hhhhhhhhhhhh.hhhhh....ee....hhhhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m63 B 247 RLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEMAKSEHRYVQAFCREILKYPDCYKSADVASPESVIDVALKRLQTGRERLFTTTDEKGNRELKKGDAILESAINAARMAISTEEKNTILSNNVKSATFDVFCELPCMDGFAEQNGKTAFYALRAGFYSAFKNTDTAKQDITKFMKDNLQAGFSGYSYQGLTNRVAQLEAQ 475
                                   256       266       276       286       296       306       316       326    || 343       353       363       373       383       393       403       413       423       433       443       453       463       473  
                                                                                                              331|                                                                                                                                        
                                                                                                               339                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4m63c1 C:6-146 automated matches                                                                                                      d4m63c2 C:147-374 automated matches                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeee.......eee...eeee........eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh...eeeeeee....eeeeeee..ee.....eee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhh......ee.....ee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhh.eeeehhhhhh.hhhhhhhhhhhhh......ee......hhhhhhhhhhh.........eehhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m63 C   6 AALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCAAAIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKC 374
                                    15        25        35       |51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  ||   333       343       353       363       373 
                                                                43|                                                                                                                                                                                                                                                                               324|                                               
                                                                 50                                                                                                                                                                                                                                                                                327                                               


Chain D from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4m63d1 D:5-146 automated matches                                                                                                    d4m63d2 D:147-374 automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..eee......eehhhhhhh....eee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.....eee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhh.eeeehhhhh...hhhhhhhhhhh.........ee......hhhhhhhhhhhhhhhhh...eehhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m63 D   5 VAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCAAAIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKC 374
                                    14        24        34     || 53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373 
                                                              40|                                                                                                                                                                                                                                                                                                                                    
                                                               50                                                                                                                                                                                                                                                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4m63e1 E:6-146 automated matches                                                                                         d4m63e2 E:147-374 automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eeeeee.......eeee.......hhhhhh......hhhhh..hhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhh...........hhhhhhhhhhhhh....hhhhhhhhhh......eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee......hhhhhhhhhhh.........eehhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m63 E   6 AALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPGDEAQSKRGILYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCAAAIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKC 374
                                    15        25        35  ||    61   ||   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
                                                           38|        65|                                                                                                                                                                                                                                                                                                                 
                                                            55         69
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M63)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M63)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  4m63
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACT1_DROME | P10987: 1n58 2hf3 2hf4 3eks 3eku 3el2 3mmv 3mn6 3mn7 3mn9 4jhd 4rwt

(-) Related Entries Specified in the PDB File

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