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(-) Description

Title :  DIMERIZATION DOMAIN OF VIBRIO PARAHEMOLYTICUS VOPL
 
Authors :  S. Namgoong, R. Dominguez
Date :  11 May 11  (Deposition) - 31 Aug 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Actin Nucleation, Filament Pointed End Binding, Type Iii Secretion System (T3Ss) Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Namgoong, M. Boczkowska, M. J. Glista, J. D. Winkelman, G. Rebowski D. R. Kovar, R. Dominguez
Mechanism Of Actin Filament Nucleation By Vibrio Vopl And Implications For Tandem W Domain Nucleation.
Nat. Struct. Mol. Biol. V. 18 1060 2011
PubMed-ID: 21873985  |  Reference-DOI: 10.1038/NSMB.2109

(-) Compounds

Molecule 1 - PROTEIN VPA1370
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB12
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: INTEIN FUSION
    Fragment: VOPL DIMERIZATION DOMAIN (UNP RESIDUES 247-484)
    Gene: VOPL, VPA1370
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 223926
    Strain: RIMD 2210633
    Synonym: ACTIN FILAMENT POINTED END-BINDING DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3RYL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Pro A:258 -Lys A:259
2Arg A:293 -Gly A:294
3Glu A:304 -His A:305
4Lys A:369 -Gly A:370
5Lys A:436 -Asn A:437
6Gly A:456 -Phe A:457
7Gly A:459 -Tyr A:460
8Pro B:258 -Lys B:259
9Gly B:294 -Leu B:295
10Leu B:295 -Thr B:296
11Arg B:352 -Glu B:353
12Asp B:360 -Glu B:361
13Glu B:361 -Lys B:362
14Asn B:364 -Arg B:365
15Arg B:365 -Glu B:366
16Lys B:369 -Gly B:370
17Asp B:371 -Ala B:372
18Gly B:456 -Phe B:457
19Gly B:459 -Tyr B:460

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RYL)

(-) Exons   (0, 0)

(no "Exon" information available for 3RYL)

(-) 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:220
 aligned with Q87GE5_VIBPA | Q87GE5 from UniProtKB/TrEMBL  Length:484

    Alignment length:238
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473        
         Q87GE5_VIBPA   244 THERLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEMAKSEHRYVQAFCREILKYPDCYKSADVASPESPKSGGGSVIDVALKRLQTGRERLFTTTDEKGNRELKKGDAILESAINAARMAISTEEKNTILSNNVKSATFEVFCELPCMDGFAEQNGKTAFYALRAGFYSAFKNTDTAKQDITKFMKDNLQAGFSGYSYQGLTNRVAQLEAQLAALSA 481
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhh...------------------.hhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ryl A 244 GHmRLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEmAKSEHRYVQAFCREILKYPD------------------SVIDVALKRLQTGRERLFTTTDEKGNRELKKGDAILESAINAARmAISTEEKNTILSNNVKSATFEVFCELPCmDGFAEQNGKTAFYALRAGFYSAFKNTDTAKQDITKFmKDNLQAGFSGYSYQGLTNRVAQLEAQLAALSA 481
                              |    253       263       273       283       293      |303       313      |  -         -     | 343       353       363       373       383       393       403       413       423       433       443     | 453       463       473        
                              |                                                   300-MSE             320                339                                         383-MSE                      412-MSE                              449-MSE                            
                            246-MSE                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q87GE5_VIBPA | Q87GE5 from UniProtKB/TrEMBL  Length:484

    Alignment length:235
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475     
         Q87GE5_VIBPA   246 ERLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEMAKSEHRYVQAFCREILKYPDCYKSADVASPESPKSGGGSVIDVALKRLQTGRERLFTTTDEKGNRELKKGDAILESAINAARMAISTEEKNTILSNNVKSATFEVFCELPCMDGFAEQNGKTAFYALRAGFYSAFKNTDTAKQDITKFMKDNLQAGFSGYSYQGLTNRVAQLEAQLAALS 480
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh...hhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhh........---------------.hhhhhhh..........................hhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ryl B 246 mRLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEmAKSEHRYVQAFCREILKYPDCYKS---------------VIDVALKRLQTGRERLFTTTDEKGNRELKKGDAILESAINAARmAISTEEKNTILSNNVKSATFEVFCELPCmDGFAEQNGKTAFYALRAGFYSAFKNTDTAKQDITKFmKDNLQAGFSGYSYQGLTNRVAQLEAQLAALS 480
                            |      255       265       275       285       295    |  305       315        |-         -    |  345       355       365       375       385       395       405      |415       425       435       445   |   455       465       475     
                          246-MSE                                               300-MSE                 324             340                                        383-MSE                      412-MSE                              449-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3RYL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q87GE5_VIBPA | Q87GE5)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.

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  Cis Peptide Bonds
    Arg A:293 - Gly A:294   [ RasMol ]  
    Arg B:352 - Glu B:353   [ RasMol ]  
    Arg B:365 - Glu B:366   [ RasMol ]  
    Asn B:364 - Arg B:365   [ RasMol ]  
    Asp B:360 - Glu B:361   [ RasMol ]  
    Asp B:371 - Ala B:372   [ RasMol ]  
    Glu A:304 - His A:305   [ RasMol ]  
    Glu B:361 - Lys B:362   [ RasMol ]  
    Gly A:456 - Phe A:457   [ RasMol ]  
    Gly A:459 - Tyr A:460   [ RasMol ]  
    Gly B:294 - Leu B:295   [ RasMol ]  
    Gly B:456 - Phe B:457   [ RasMol ]  
    Gly B:459 - Tyr B:460   [ RasMol ]  
    Leu B:295 - Thr B:296   [ RasMol ]  
    Lys A:369 - Gly A:370   [ RasMol ]  
    Lys A:436 - Asn A:437   [ RasMol ]  
    Lys B:369 - Gly B:370   [ RasMol ]  
    Pro A:258 - Lys A:259   [ RasMol ]  
    Pro B:258 - Lys B:259   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q87GE5_VIBPA | Q87GE5: 3m1f 3seo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RYL)