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(-) Description

Title :  CRYSTAL STRUCTURE OF FRAC WITH POC BOUND (CRYSTAL FORM II)
 
Authors :  J. M. M. Caaveiro, K. Tanaka, K. Tsumoto
Date :  19 Jun 14  (Deposition) - 04 Mar 15  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Toxin, Actinoporin, Pore-Forming Toxin, Membrane Lipids, Phosphocholine, Lipid-Protein Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tanaka, J. M. M. Caaveiro, K. Morante, J. M. Gonzalez-Manas, K. Tsumoto
Structural Basis For Self-Assembly Of A Cytolytic Pore Line By Protein And Lipid
Nat Commun V. 6 6337 2015
PubMed-ID: 25716479  |  Reference-DOI: 10.1038/NCOMMS7337
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRAGACEATOXIN C
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEM-T
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: STRAWBERRY ANEMONE
    Organism Scientific: ACTINIA FRAGACEA
    Organism Taxid: 396334
    Synonym: FRAC

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric Unit (4, 23)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3PC8Ligand/IonPHOSPHOCHOLINE
4SO412Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3PC-1Ligand/IonPHOSPHOCHOLINE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3PC-1Ligand/IonPHOSPHOCHOLINE
4SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3PC-1Ligand/IonPHOSPHOCHOLINE
4SO43Ligand/IonSULFATE ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3PC-1Ligand/IonPHOSPHOCHOLINE
4SO45Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:54 , THR A:84 , GLY A:85 , SER A:105 , PRO A:107 , TYR A:108 , TYR A:113 , TYR A:133 , TYR A:137 , TYR A:138 , HOH A:303 , HOH A:318 , HOH A:348binding site for residue PC A 201
02AC2SOFTWARETYR A:113 , SER A:114 , TRP A:116 , TYR A:137 , PRO A:142 , GOL A:206 , HOH A:304binding site for residue PC A 202
03AC3SOFTWARETRP A:112 , TYR A:113binding site for residue PC A 203
04AC4SOFTWAREARG A:120 , TYR A:122 , LYS A:123 , HOH A:366 , HOH A:401binding site for residue SO4 A 204
05AC5SOFTWARELYS A:30 , ARG A:31 , HOH A:305 , HOH A:377 , HOH A:454binding site for residue SO4 A 205
06AC6SOFTWARETRP A:112 , TYR A:113 , SER A:114 , ARG A:144 , PC A:202 , HOH A:302binding site for residue GOL A 206
07AC7SOFTWAREARG B:53 , SER B:54 , THR B:84 , GLY B:85 , SER B:105 , PRO B:107 , TYR B:108 , TYR B:113 , TYR B:133 , TYR B:137 , TYR B:138 , HOH B:302 , HOH B:325 , HOH B:352binding site for residue PC B 201
08AC8SOFTWARETYR B:113 , SER B:114 , TRP B:116 , TYR B:137 , HOH B:311 , HOH B:394binding site for residue PC B 202
09AC9SOFTWARELYS A:30 , TYR A:108 , HOH A:307 , ARG B:120 , TYR B:122 , LYS B:123 , HOH B:303 , HOH B:313binding site for residue SO4 B 203
10AD1SOFTWAREARG B:144 , HOH B:439 , GLY D:124 , GLN D:125binding site for residue SO4 B 204
11AD2SOFTWAREASP A:109 , TRP A:112 , LYS B:123binding site for residue ACT B 205
12AD3SOFTWAREARG C:53 , SER C:54 , GLY C:85 , SER C:105 , PRO C:107 , TYR C:108 , TYR C:113 , TYR C:133 , TYR C:137 , TYR C:138 , SO4 C:202 , HOH C:301 , HOH C:311 , HOH C:351binding site for residue PC C 201
13AD4SOFTWAREARG C:53 , GLN C:130 , TYR C:133 , TYR C:138 , PC C:201binding site for residue SO4 C 202
14AD5SOFTWAREVAL C:29 , LYS C:30 , LYS C:77 , ARG C:79 , GLY C:80 , HOH C:303 , HOH C:306 , HOH C:377 , HOH D:334binding site for residue SO4 C 203
15AD6SOFTWAREARG C:120 , TYR C:122 , LYS C:123 , HOH C:413 , HOH C:441binding site for residue SO4 C 204
16AD7SOFTWAREARG D:53 , SER D:54 , GLY D:85 , SER D:105 , PRO D:107 , TYR D:108 , TYR D:113 , TYR D:133 , TYR D:137 , TYR D:138 , SO4 D:203 , HOH D:304 , HOH D:330 , HOH D:372binding site for residue PC D 201
17AD8SOFTWARETRP D:112 , TYR D:113 , SER D:114 , TRP D:116 , TYR D:137 , PRO D:142 , HOH D:390binding site for residue PC D 202
18AD9SOFTWAREARG D:53 , GLN D:130 , TYR D:133 , TYR D:138 , PC D:201binding site for residue SO4 D 203
19AE1SOFTWAREASN D:28 , VAL D:29 , LYS D:30 , LYS D:77 , ARG D:79 , GLY D:80 , HOH D:337 , HOH D:343binding site for residue SO4 D 204
20AE2SOFTWARETHR B:56 , ASN B:78 , ARG B:79 , SER D:167 , HOH D:318 , HOH D:336binding site for residue SO4 D 205
21AE3SOFTWAREARG C:79 , ARG D:120 , TYR D:122 , LYS D:123 , HOH D:405binding site for residue SO4 D 206
22AE4SOFTWARELYS D:178binding site for residue SO4 D 207
23AE5SOFTWAREASN D:28 , ARG D:79binding site for residue ACT D 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TSN)

(-) Sequences/Alignments

Asymmetric 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsn A   2 ADVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsn B   2 ADVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        


Chain C from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhh..hhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsn C   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


Chain D from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.hhh..hhhhhhhhhh.....eeeeeeee.....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsn D   2 ADVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   Legend:   → Mismatch (orange background)
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  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 4TSN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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  4tsn
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  ACTPC_ACTFR | B9W5G6
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACTPC_ACTFR | B9W5G6: 3lim 3vwi 3w9p 3zwg 3zwj 4tsl 4tso 4tsp 4tsq 4tsy 4wdc 5bpg 5gwf

(-) Related Entries Specified in the PDB File

3vwi THE SAME PROTEIN IN THE WATER-SOLUBLE STATE (CRYSTAL FORM I)
3w9p THE SAME PROTEIN IN THE WATER-SOLUBLE STATE (CRYSTAL FORM II)
4tsl
4tso
4tsp
4tsq
4tsy