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(-) Description

Title :  CRYSTAL STRUCTURE OF FRAC WITH LIPIDS
 
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 :  3.14
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
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 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 32)

Asymmetric Unit (3, 32)
No.NameCountTypeFull Name
1HTO1Ligand/IonHEPTANE-1,2,3-TRIOL
2HXJ12Ligand/Ion2-[[(E,2S,3R)-2-(HEXANOYLAMINO)-3-OXIDANYL-DEC-4-ENOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL-TRIMETHYL-AZANIUM
3SO419Ligand/IonSULFATE ION
Biological Unit 1 (3, 64)
No.NameCountTypeFull Name
1HTO2Ligand/IonHEPTANE-1,2,3-TRIOL
2HXJ24Ligand/Ion2-[[(E,2S,3R)-2-(HEXANOYLAMINO)-3-OXIDANYL-DEC-4-ENOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL-TRIMETHYL-AZANIUM
3SO438Ligand/IonSULFATE ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:53 , SER A:54 , THR A:84 , GLY A:85 , PRO A:107 , TYR A:108 , TYR A:113 , TYR A:133 , TYR A:137 , SO4 A:204binding site for residue HXJ A 201
02AC2SOFTWAREASN A:111 , TRP A:112 , TYR A:113 , SER A:114 , TRP A:116 , TYR A:137 , PRO A:142binding site for residue HXJ A 202
03AC3SOFTWAREARG A:120 , TYR A:122 , LYS A:123binding site for residue SO4 A 203
04AC4SOFTWAREARG A:53 , GLN A:130 , TYR A:133 , TYR A:138 , HXJ A:201binding site for residue SO4 A 204
05AC5SOFTWARETRP A:149 , ARG A:161 , HIS A:175 , HIS B:63binding site for residue SO4 A 205
06AC6SOFTWARETHR A:44 , SER A:95 , HTO A:209 , LYS C:123binding site for residue SO4 A 206
07AC7SOFTWAREARG A:79 , HIS D:169binding site for residue SO4 A 207
08AC8SOFTWARETYR A:51 , ARG A:53binding site for residue SO4 A 208
09AC9SOFTWARELYS A:43 , SER A:95 , ASP A:96 , SO4 A:206 , TYR C:156binding site for residue HTO A 209
10AD1SOFTWAREVAL A:29 , ARG A:31 , SER A:166 , SER A:167 , GLY A:168 , THR B:56 , ASN B:78 , ARG B:79 , HOH B:301binding site for residue HXJ B 201
11AD2SOFTWARESER B:54 , THR B:84 , GLY B:85 , TYR B:108 , TYR B:113 , TYR B:133 , TYR B:137 , SO4 B:205binding site for residue HXJ B 202
12AD3SOFTWAREASN B:111 , TRP B:112 , TYR B:113 , TRP B:116 , TYR B:137 , PRO B:142 , SO4 B:207 , HOH B:303binding site for residue HXJ B 203
13AD4SOFTWAREARG B:120 , TYR B:122 , LYS B:123binding site for residue SO4 B 204
14AD5SOFTWAREARG B:53 , GLN B:130 , TYR B:133 , TYR B:138 , HXJ B:202binding site for residue SO4 B 205
15AD6SOFTWAREARG B:161 , GLU B:173 , HIS B:175 , HIS C:63binding site for residue SO4 B 206
16AD7SOFTWARESER B:114 , TRP B:116 , ARG B:144 , HXJ B:203 , HOH B:303binding site for residue SO4 B 207
17AD8SOFTWARETRP B:149 , HIS B:150 , SER B:151 , ARG C:127binding site for residue SO4 B 208
18AD9SOFTWAREARG B:31 , SER B:166 , SER B:167 , GLY B:168 , THR C:56 , ASN C:78 , ARG C:79binding site for residue HXJ C 201
19AE1SOFTWARESER C:54 , THR C:84 , GLY C:85 , TYR C:108 , TRP C:112 , TYR C:113 , TYR C:133 , TYR C:137 , SO4 C:206binding site for residue HXJ C 202
20AE2SOFTWAREASN C:111 , TRP C:112 , TYR C:113 , TRP C:116 , TYR C:137 , PRO C:142 , SO4 C:208binding site for residue HXJ C 203
21AE3SOFTWARELEU C:26 , ARG C:31 , TYR C:110 , SER C:166 , SER C:167 , GLY C:168 , THR D:56 , ASN D:78 , ARG D:79 , VAL D:82binding site for residue HXJ C 204
22AE4SOFTWAREARG C:120 , VAL C:121 , TYR C:122 , LYS C:123binding site for residue SO4 C 205
23AE5SOFTWAREARG C:53 , GLN C:130 , TYR C:133 , TYR C:138 , HXJ C:202binding site for residue SO4 C 206
24AE6SOFTWAREARG C:161 , GLU C:173 , HIS C:175 , HOH C:307 , HIS D:63binding site for residue SO4 C 207
25AE7SOFTWARESER C:114 , ARG C:144 , HXJ C:203binding site for residue SO4 C 208
26AE8SOFTWARESER D:54 , ALA D:83 , THR D:84 , GLY D:85 , TYR D:108 , TRP D:112 , TYR D:113 , TYR D:133 , TYR D:137 , SO4 D:205 , HOH D:303binding site for residue HXJ D 201
27AE9SOFTWAREASN D:111 , TRP D:112 , TYR D:113 , TRP D:116 , TYR D:137 , PRO D:142 , SO4 D:207binding site for residue HXJ D 202
28AF1SOFTWAREASN A:78 , ARG A:79 , ARG D:31 , TYR D:110 , SER D:166 , SER D:167 , GLY D:168binding site for residue HXJ D 203
29AF2SOFTWAREARG D:120 , TYR D:122 , LYS D:123binding site for residue SO4 D 204
30AF3SOFTWAREARG D:53 , GLN D:130 , TYR D:133 , TYR D:138 , HXJ D:201binding site for residue SO4 D 205
31AF4SOFTWAREHIS A:63 , ARG D:161 , GLU D:173 , HIS D:175binding site for residue SO4 D 206
32AF5SOFTWARESER D:114 , TRP D:116 , ARG D:144 , HXJ D:202binding site for residue SO4 D 207

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TSY)

(-) 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsy A   4 VAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsy B   4 VAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsy C   4 VAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain D from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsy D   4 VAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
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  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 4TSY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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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 4tsn 4tso 4tsp 4tsq 4wdc 5bpg 5gwf

(-) Related Entries Specified in the PDB File

3vwi THE SAME PROTEIN IN THE WATER-SOLUBLE STATE (CRYSTAL FORM I)
3wp9 THE SAME PROTEIN IN THE WATER-SOLUBLE STATE (CRYSTAL FORM II)
4tsl
4tsn
4tso
4tsp
4tsq