3VWI - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF FRAC IN THE MONOMERIC FORM

Authors :   K. Tanaka, K. Morante, J. M. M. Caaveiro, J. M. Gonzalez-Manas, K. Tsumo

Date :   23 Aug 12 (Deposition) - 28 Aug 13 (Release) - 03 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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 :   Beta-Sandwich, Amphipathic Alpha-Helix, Actinoporin, Pore-Forming Toxin, Citolysin, Membrane Lipids, Secreted Protein, Lipid Raft, Toxin (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)

Molecule 1 - FRAGACEATOXIN C
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEM-T
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FRAC
	Organism Common	:	STRAWBERRY ANEMONE
	Organism Scientific	:	ACTINIA FRAGACEA
	Organism Taxid	:	396334
	Synonym	:	FRAC

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	CL	8	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	NH4	2	Ligand/Ion	AMMONIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NH4	1	Ligand/Ion	AMMONIUM ION
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	NH4	-1	Ligand/Ion	AMMONIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NH4	1	Ligand/Ion	AMMONIUM ION
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NH4	-1	Ligand/Ion	AMMONIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:113 , SER A:114 , TRP A:116 , HOH B:370	BINDING SITE FOR RESIDUE CL A 201
02	AC2	SOFTWARE	HOH A:473 , SO4 B:204	BINDING SITE FOR RESIDUE NH4 A 202
03	AC3	SOFTWARE	TYR B:113 , SER B:114 , TRP B:116 , HOH B:440	BINDING SITE FOR RESIDUE CL B 201
04	AC4	SOFTWARE	LEU B:61 , HOH B:324	BINDING SITE FOR RESIDUE CL B 202
05	AC5	SOFTWARE	PHE B:16 , ASP B:17 , LYS C:64 , HOH C:381	BINDING SITE FOR RESIDUE CL B 203
06	AC6	SOFTWARE	LYS A:30 , NH4 A:202 , HIS B:63 , LYS B:64	BINDING SITE FOR RESIDUE SO4 B 204
07	AC7	SOFTWARE	GLY B:15 , PHE B:16 , TRP B:149 , GLU B:173 , HOH B:312 , HOH B:313 , HOH B:327 , HOH B:374 , HOH B:376 , MET C:94 , GLN C:125	BINDING SITE FOR RESIDUE GOL B 205
08	AC8	SOFTWARE	TRP B:149 , ARG B:161 , HOH B:327 , GLY C:97 , ASN C:98 , LYS C:123	BINDING SITE FOR RESIDUE GOL B 206
09	AC9	SOFTWARE	TYR C:113 , SER C:114 , TRP C:116 , HOH C:400	BINDING SITE FOR RESIDUE CL C 201
10	BC1	SOFTWARE	LYS C:123	BINDING SITE FOR RESIDUE CL C 202
11	BC2	SOFTWARE	SO4 D:203	BINDING SITE FOR RESIDUE NH4 C 203
12	BC3	SOFTWARE	LEU D:61 , HOH D:307	BINDING SITE FOR RESIDUE CL D 201
13	BC4	SOFTWARE	TYR D:113 , SER D:114 , TRP D:116 , HOH D:387	BINDING SITE FOR RESIDUE CL D 202
14	BC5	SOFTWARE	LYS C:30 , NH4 C:203 , HIS D:63 , LYS D:64 , HOH D:421	BINDING SITE FOR RESIDUE SO4 D 203

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

(no "Cis Peptide Bond" information available for 3VWI)

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

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

(no "Exon" information available for 3VWI)

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
 aligned with ACTPC_ACTFR | B9W5G6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       
          ACTPC_ACTFR     3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
               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
                 3vwi 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:177
 aligned with ACTPC_ACTFR | B9W5G6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       
          ACTPC_ACTFR     3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
               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
                 3vwi B   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain C from PDB  Type:PROTEIN  Length:177
 aligned with ACTPC_ACTFR | B9W5G6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       
          ACTPC_ACTFR     3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
               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
                 3vwi 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:177
 aligned with ACTPC_ACTFR | B9W5G6 from UniProtKB/Swiss-Prot  Length:179

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

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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ACTPC_ACTFR | B9W5G6)

molecular function
	GO:0015267	channel activity	Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
biological process
	GO:0006812	cation transport	The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0052331	hemolysis in other organism involved in symbiotic interaction	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another, where two organisms are in a symbiotic interaction.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0046931	pore complex assembly	The aggregation, arrangement and bonding together of a set of components to form a pore complex. A pore complex is a small opening in a membrane that allows the passage of liquids and/or gases.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0042151	nematocyst	An organelle found in cnidoblast (nematoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the cnidocyst) is stimulated by a prey or another stimulus.
	GO:0044218	other organism cell membrane	The cell membrane of a secondary organism with which the first organism is interacting.
	GO:0044279	other organism membrane	A membrane of a secondary organism with which the first organism is interacting.
	GO:0046930	pore complex	Any small opening in a membrane that allows the passage of gases and/or liquids.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vwi)

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	3vwi
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	ACTPC_ACTFR \| B9W5G6	:	3lim 3w9p 3zwg 3zwj 4tsl 4tsn 4tso 4tsp 4tsq 4tsy 4wdc 5bpg 5gwf

3lim	CRYSTAL STRUCTURE OF FRAC IN THE OLIGOMERIC (9-MER) FORM

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Ligands, Modified Residues, Ions (4, 14)

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