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(-) Description

Title :  CRYSTAL STRUCTURE OF FRAC WITH DHPC BOUND (CRYSTAL FORM III)
 
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 :  1.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (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, E, F
    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

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 31)

Asymmetric Unit (4, 31)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2HXG16Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC8Ligand/IonPHOSPHOCHOLINE
4SCN5Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HXG5Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC-1Ligand/IonPHOSPHOCHOLINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HXG4Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC-1Ligand/IonPHOSPHOCHOLINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HXG2Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC-1Ligand/IonPHOSPHOCHOLINE
4SCN-1Ligand/IonTHIOCYANATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HXG2Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC-1Ligand/IonPHOSPHOCHOLINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HXG2Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC-1Ligand/IonPHOSPHOCHOLINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HXG1Ligand/Ion1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PC-1Ligand/IonPHOSPHOCHOLINE
4SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:53 , SER A:54 , THR A:84 , GLY A:85 , VAL A:87 , SER A:105 , PRO A:107 , TYR A:108 , TRP A:112 , TYR A:113 , TYR A:133 , TYR A:137 , HXG A:203 , HOH A:366 , HOH A:425 , HOH A:440binding site for residue HXG A 201
02AC2SOFTWARETRP A:112 , TYR A:113 , TRP A:116 , TYR A:137 , TYR A:138 , HXG A:204 , HOH A:382 , HOH A:407 , HOH A:466binding site for residue HXG A 202
03AC3SOFTWAREARG A:53 , GLN A:130 , TYR A:133 , GLU A:134 , TYR A:138 , HXG A:201 , PC A:207binding site for residue HXG A 203
04AC4SOFTWAREASN A:111 , TRP A:112 , SER A:114 , ARG A:144 , HXG A:202 , PC A:207 , HOH A:382 , HOH A:460binding site for residue HXG A 204
05AC5SOFTWAREVAL A:121 , TYR A:122 , LYS A:123 , ARG A:140 , LEU A:154 , TYR A:156 , HOH A:410 , HOH A:420 , ILE E:9 , ASP E:17 , VAL E:18 , THR E:21 , VAL E:22 , ALA E:25 , ILE E:59 , LEU E:72 , HOH E:357binding site for residue HXG A 205
06AC6SOFTWAREASN A:78 , VAL A:82 , THR A:84 , HOH A:392 , HOH A:440 , ASN F:111 , TRP F:112 , TYR F:113 , SER F:114binding site for residue PC A 206
07AC7SOFTWARETYR A:138 , HIS A:139 , HXG A:203 , HXG A:204binding site for residue PC A 207
08AC8SOFTWARELYS A:43 , MET A:94 , ASP A:96 , GLY A:97 , ASN A:98binding site for residue SCN A 208
09AC9SOFTWARETRP B:112 , TYR B:113 , TRP B:116 , TYR B:137 , TYR B:138 , HXG B:202 , HXG B:204 , HOH B:355 , HOH B:400 , HOH B:407binding site for residue HXG B 201
10AD1SOFTWAREARG B:53 , SER B:54 , THR B:84 , GLY B:85 , VAL B:87 , SER B:105 , PRO B:107 , TYR B:108 , TYR B:113 , TYR B:133 , TYR B:137 , TYR B:138 , HXG B:201 , HXG B:203 , HOH B:383binding site for residue HXG B 202
11AD2SOFTWAREARG B:53 , GLN B:130 , TYR B:133 , GLU B:134 , TYR B:138 , HXG B:202 , HXG B:204 , CL B:206binding site for residue HXG B 203
12AD3SOFTWAREASN B:111 , TRP B:112 , SER B:114 , ARG B:144 , HXG B:201 , HXG B:203 , HOH B:355 , HXG E:201binding site for residue HXG B 204
13AD4SOFTWARELYS B:43 , MET B:94 , ASP B:96 , GLY B:97 , ASN B:98 , TYR B:156binding site for residue SCN B 205
14AD5SOFTWAREHIS B:139 , HXG B:203binding site for residue CL B 206
15AD6SOFTWARETRP C:112 , TYR C:113 , SER C:114 , TRP C:116 , TYR C:137 , HOH C:393 , HOH C:409binding site for residue HXG C 201
16AD7SOFTWAREARG C:53 , SER C:54 , THR C:84 , GLY C:85 , VAL C:87 , SER C:105 , PRO C:107 , TYR C:108 , TYR C:113 , TYR C:133 , TYR C:137 , TYR C:138 , PC C:203 , HOH C:363binding site for residue HXG C 202
17AD8SOFTWAREARG C:53 , GLN C:130 , TYR C:133 , TYR C:138 , HXG C:202 , ARG D:53binding site for residue PC C 203
18AD9SOFTWARETRP D:112 , TYR D:113 , SER D:114 , TRP D:116 , TYR D:137 , TYR D:138 , HOH D:400 , HOH D:405binding site for residue HXG D 201
19AE1SOFTWARESER D:54 , ALA D:83 , THR D:84 , GLY D:85 , VAL D:87 , SER D:105 , PRO D:107 , TYR D:108 , TYR D:113 , TYR D:133 , TYR D:137 , PC D:203 , HOH D:366 , HOH D:404binding site for residue HXG D 202
20AE2SOFTWAREARG D:53 , TYR D:133 , GLU D:134 , TYR D:138 , HXG D:202 , HOH D:404binding site for residue PC D 203
21AE3SOFTWARELYS D:43 , MET D:94 , ASP D:96 , GLY D:97 , ASN D:98 , TYR D:156binding site for residue SCN D 204
22AE4SOFTWAREHXG B:204 , TRP E:112 , TYR E:113 , TRP E:116 , TYR E:137 , PC E:203 , HOH E:345 , HOH E:385binding site for residue HXG E 201
23AE5SOFTWARESER E:54 , ALA E:83 , THR E:84 , GLY E:85 , VAL E:87 , SER E:105 , PRO E:107 , TYR E:108 , TYR E:113 , TYR E:133 , TYR E:137 , PC E:204 , HOH E:354binding site for residue HXG E 202
24AE6SOFTWARELYS D:64 , ASN E:111 , TRP E:112 , SER E:114 , ARG E:144 , HXG E:201 , HOH E:345 , HOH E:355binding site for residue PC E 203
25AE7SOFTWAREARG E:53 , GLN E:130 , TYR E:133 , GLU E:134 , TYR E:138 , HXG E:202binding site for residue PC E 204
26AE8SOFTWARELYS E:43 , MET E:94 , ASP E:96 , GLY E:97 , ASN E:98binding site for residue SCN E 205
27AE9SOFTWARETRP F:112 , TYR F:113 , SER F:114 , TRP F:116 , TYR F:137 , TYR F:138binding site for residue HXG F 201
28AF1SOFTWARESER F:54 , GLY F:85 , VAL F:87 , SER F:105 , PRO F:107 , TYR F:108 , TYR F:113 , TYR F:133 , TYR F:137 , PC F:203 , HOH F:359binding site for residue PC F 202
29AF2SOFTWAREARG F:53 , TYR F:113 , GLN F:130 , TYR F:133 , TYR F:138 , PC F:202binding site for residue PC F 203
30AF3SOFTWARETRP B:149 , HIS B:150 , SER B:151 , ARG B:161 , PHE F:16 , ASP F:17 , HOH F:304binding site for residue SCN F 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TSQ)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsq A   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


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.....eeeeeeee.....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsq 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.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsq 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.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tsq D   2 ADVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        


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


Chain F from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               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
                 4tsq F   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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    Protein Cavities: castP
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ACTPC_ACTFR | B9W5G6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4tsy 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
4tsy