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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CYTOLETHAL DISTENDING TOXIN (CDT) FROM ACTINOBACILLUS ACTINOMYCETEMCOMITANS

Authors :   T. Yamada, J. Komoto, K. Saiki, K. Konishi, F. Takusagawa

Date :   16 Nov 05 (Deposition) - 28 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Cytolethal Distending Toxin, Cdt, Actinobacillus Actinomycetemcomitans, Crystal Structure, Oligomerization, Stability And Toxic Activity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Yamada, J. Komoto, K. Saiki, K. Konishi, F. Takusagawa
Variation Of Loop Sequence Alters Stability Of Cytolethal Distending Toxin (Cdt): Crystal Structure Of Cdt From Actinobacillus Actinomycetemcomitans
Protein Sci. V. 15 362 2006
PubMed-ID: 16434747 | Reference-DOI: 10.1110/PS.051790506
(for further references see the PDB file header)

Molecule 1 - CYTOLETHAL DISTENDING TOXIN A
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	A19-47CDT
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CDTA
	Organism Scientific	:	AGGREGATIBACTER ACTINOMYCETEMCOMITANS
	Organism Taxid	:	714
	Synonym	:	CDT A

Molecule 2 - CYTOLETHAL DISTENDING TOXIN B
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	A19-47CDT
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CDTB
	Organism Scientific	:	AGGREGATIBACTER ACTINOMYCETEMCOMITANS
	Organism Taxid	:	714
	Synonym	:	CDT B

Molecule 3 - CYTOLETHAL DISTENDING TOXIN C
	Chains	:	C, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	A19-47CDT
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CDTC
	Organism Scientific	:	AGGREGATIBACTER ACTINOMYCETEMCOMITANS
	Organism Taxid	:	714
	Synonym	:	CDT C

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2F2F)

(no "Site" information available for 2F2F)

Asymmetric Unit

No.	Residues
1	A:137	-	A:150
2	A:179	-	A:198
3	C:135	-	C:149
4	D:137	-	D:150
5	D:179	-	D:198
6	F:96	-	F:107
7	F:135	-	F:149

Asymmetric Unit

No.	Residues
1	Phe F:99	-	Pro F:100

(no "SAP(SNP)/Variant" information available for 2F2F)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	CDTA_AGGAC	122-211	2	A:123-212 D:123-212

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	CDTA_AGGAC	122-211	1	A:123-212 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	CDTA_AGGAC	122-211	1	- D:123-212

(no "Exon" information available for 2F2F)

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:153
 aligned with CDTA_AGGAC | O87120 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:153
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
           CDTA_AGGAC    70 PSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKIEPGKHREYFRFVNQSLGTCIEAYGNGLIHDTCSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSPTYYSTVTLSTCDGATEPLRDQTWYLAPPVLEATAVN 222
               SCOP domains d2f2fa1 A:71-223 Cytolethal distending toxin subunit A                                                                                                    SCOP domains
               CATH domains 2f2fA00 A:71-223  [code=2.80.10.50, no name defined]                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeee...eeeee........eeeee.hhhhhhhhhh.eeeee......eeeee.....eeeee..eeeee.....hhhh.eeeee.....eeeee.....eeee........eeeeee............eeeee.....ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------RICIN_B_LECTIN  PDB: A:123-212 UniProt: 122-211                                           ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2f A  71 PSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKIEPGKHREYFRFVNQSLGTCIEAYGNGLIHDTCSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSPTYYSTVTLSTCDGATEPLRDQTWYLAPPVLEATAVN 223
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with Q7DK12_AGGAC | Q7DK12 from UniProtKB/TrEMBL  Length:283

    Alignment length:261
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 
         Q7DK12_AGGAC    23 NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFTSSPSSPERRGYSWMVVGDFNRAPVNLEAALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVHDR 283
               SCOP domains d2f2fb1 B:23-283 Cytolethal distending toxin subunit B                                                                                                                                                                                                                SCOP domains
               CATH domains 2f2fB00 B:23-283  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee.......hhhhhhhhhhhhhh......eeeee.........ee............eeeeee........eeeeeee..........eeeee.....eeeee...........eeeeee..eeeeeee.......hhhhhhhhhhhhhh....hhhhhh.eeeeeee...hhhhhhhhhh.hhhhhhh.eee.............eeeeee.......hhhhh.eeeee.hhhh..........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2f B  23 NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFTSSPSSPERRGYSWMVVGDFNRAPVNLEAALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVHDR 283
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with Q7DK11_AGGAC | Q7DK11 from UniProtKB/TrEMBL  Length:186

    Alignment length:154
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
         Q7DK11_AGGAC    25 DPTTYPDVELSPPPRISLRSLLTAQPIKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFPGEGTTDCKDIDHTVFNLIPTNTGAFLIKDALLGFCMTSHDFDDLRLEPCGISVSGRTFSLAYQWGILPPFGPSKILRP 178
               SCOP domains d2f2fc1 C:25-178 Cytolethal distending toxin subunit C                                                                                                     SCOP domains
               CATH domains 2f2fC00 C:25-178  [code=2.80.10.50, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee...............hhhhhheeeee.............eeeeee.....eee......eee..hhhhhheeeee.....eeeee.....eee.......eee.........eehhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2f C  25 DPTTYPDVELSPPPRISLRSLLTAQPIKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFPGEGTTDCKDIDHTVFNLIPTNTGAFLIKDALLGFCMTSHDFDDLRLEPCGISVSGRTFSLAYQWGILPPFGPSKILRP 178
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain D from PDB  Type:PROTEIN  Length:153
 aligned with CDTA_AGGAC | O87120 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:153
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
           CDTA_AGGAC    70 PSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKIEPGKHREYFRFVNQSLGTCIEAYGNGLIHDTCSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSPTYYSTVTLSTCDGATEPLRDQTWYLAPPVLEATAVN 222
               SCOP domains d2f2fd_ D: Cytolethal distending toxin subunit A                                                                                                          SCOP domains
               CATH domains 2f2fD00 D:71-223  [code=2.80.10.50, no name defined]                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeee...eeeee........eeeee.hhhhhhhhhh.eeeee......eeeee.....eeeee..eeeee.....hhhh.eeeee.....eeeee.....eeee........eeeeee.............eeee.....ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------RICIN_B_LECTIN  PDB: D:123-212 UniProt: 122-211                                           ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2f D  71 PSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKIEPGKHREYFRFVNQSLGTCIEAYGNGLIHDTCSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSPTYYSTVTLSTCDGATEPLRDQTWYLAPPVLEATAVN 223
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain E from PDB  Type:PROTEIN  Length:261
 aligned with Q7DK12_AGGAC | Q7DK12 from UniProtKB/TrEMBL  Length:283

    Alignment length:261
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 
         Q7DK12_AGGAC    23 NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFTSSPSSPERRGYSWMVVGDFNRAPVNLEAALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVHDR 283
               SCOP domains d2f2fe_ E: Cytolethal distending toxin subunit B                                                                                                                                                                                                                      SCOP domains
               CATH domains 2f2fE00 E:23-283  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee.......hhhhhhhhhhhhhh......eeeee.........ee............eeeeee........eeeeeee..........eeeee.....eeeee...........eeeeee..eeeeeee.......hhhhhhhhhhhhhh....hhhhhhheeeeeee...hhhhhhhhhh.hhhhhh..eee.............eeeeee.......hhhhh.eeeee.hhhh..........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2f E  23 NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFTSSPSSPERRGYSWMVVGDFNRAPVNLEAALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVHDR 283
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain F from PDB  Type:PROTEIN  Length:154
 aligned with Q7DK11_AGGAC | Q7DK11 from UniProtKB/TrEMBL  Length:186

    Alignment length:154
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
         Q7DK11_AGGAC    25 DPTTYPDVELSPPPRISLRSLLTAQPIKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFPGEGTTDCKDIDHTVFNLIPTNTGAFLIKDALLGFCMTSHDFDDLRLEPCGISVSGRTFSLAYQWGILPPFGPSKILRP 178
               SCOP domains d2f2ff_ F: Cytolethal distending toxin subunit C                                                                                                           SCOP domains
               CATH domains 2f2fF00 F:25-178  [code=2.80.10.50, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee...............hhhhhheeeee.............eeeeee.....ee........ee..hhhhhheeeee.....eeeee.....eee.......eee.........eehhh.eeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2f F  25 DPTTYPDVELSPPPRISLRSLLTAQPIKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFPGEGTTDCKDIDHTVFNLIPTNTGAFLIKDALLGFCMTSHDFDDLRLEPCGISVSGRTFSLAYQWGILPPFGPSKILRP 178
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

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 "Pfam Domain" information available for 2F2F)

Asymmetric Unit(hide GO term definitions)

Chain A,D (CDTA_AGGAC | O87120)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,E (Q7DK12_AGGAC | Q7DK12)

biological process
	GO:0044072		negative regulation by symbiont of host cell cycle		The process in which a symbiont organism stops, prevents or reduces the rate or extent of its host's progression through its cell cycle via direct interactions with the host cell macromolecular machinery.
	GO:0009405		pathogenesis		The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.

Chain C,F (Q7DK11_AGGAC | Q7DK11)

biological process
	GO:0009405		pathogenesis		The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.

Asymmetric Unit
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(no "Sites" information available for 2f2f)

	Cis Peptide Bonds
		Phe F:99 - Pro F:100	[ RasMol ]

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (7, 7)

Cis Peptide Bonds (1, 1)

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