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Title :   STRUCTURE OF BOTULINUM NEUROTOXIN B BINDING DOMAIN IN COMPLEX WITH BOTH SYNAPTOTAGMIN II AND GD1A

Authors :   R. P. A. Berntsson, L. Peng, M. Dong, P. Stenmark

Date :   23 Apr 13 (Deposition) - 03 Jul 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Toxin Binding Domain, Synaptotagmin And Ganglioside, Signaling Protein-Toxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. P. Berntsson, L. Peng, M. Dong, P. Stenmark
Structure Of Dual Receptor Binding To Botulinum Neurotoxin B.
Nat Commun V. 4 2058 2013
PubMed-ID: 23807078 | Reference-DOI: 10.1038/NCOMMS3058

Molecule 1 - BOTULINUM NEUROTOXIN TYPE B
	Chains	:	A, B
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 857-1291
	Gene	:	BOTB
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM
	Organism Taxid	:	1491
	Synonym	:	BONT/B, BONTOXILYSIN-B, BOTULINUM NEUROTOXIN B LIGHT CHAIN, BOTULINUM NEUROTOXIN B HEAVY CHAIN

Molecule 2 - SYNAPTOTAGMIN-2
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 8-61
	Gene	:	SYT2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SYNAPTOTAGMIN II, SYTII

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 15)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	NGA	2	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	4	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	2	Ligand/Ion	O-SIALIC ACID

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	2	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:1105 , GLU A:1190 , ILE A:1240 , HIS A:1241 , SER A:1260 , TRP A:1262 , TYR A:1263 , ASN A:1273 , LYS A:1275 , GLY A:1277 , HOH A:1490 , HOH A:1514 , SER B:984 , PHE B:986 , LEU B:1022 , GLU B:1023 , SER B:1024 , ASN B:1025 , THR B:1026 , HOH B:1442	BINDING SITE FOR LINKED RESIDUES A 1 to 6
2	AC7	SOFTWARE	GLU A:997 , PHE A:1101 , LYS A:1106	BINDING SITE FOR RESIDUE CL
3	AC8	SOFTWARE	ARG B:1001 , LYS B:1106	BINDING SITE FOR RESIDUE CL
4	AC9	SOFTWARE	GLU B:1033 , HOH B:1466 , HOH B:1471 , HOH B:1474 , HOH B:1514	BINDING SITE FOR RESIDUE MG
5	BC1	SOFTWARE	SER A:984 , VAL A:985 , PHE A:986 , LEU A:1022 , SER A:1024 , ASN A:1025 , THR A:1026 , GLY B:1104 , ASN B:1105 , GLU B:1190 , ILE B:1240 , HIS B:1241 , SER B:1260 , TRP B:1262 , TYR B:1263 , ASN B:1273 , LYS B:1275 , LEU B:1276 , GLY B:1277 , HOH B:1451	BINDING SITE FOR LINKED RESIDUES B 1 to 6

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

Asymmetric Unit

No.	Residues
1	Lys A:1270	-	Pro A:1271
2	Lys B:1270	-	Pro B:1271

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

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

(no "Exon" information available for 4KBB)

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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kbba1 A:862-1079 Botulinum neurotoxin                                                                                                                                                                                   d4kbba2 A:1080-1291 Botulinum neurotoxin                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eee......eeee....ee....eeee.......eeee.............eeeeeeee.......hhhhhhhheeeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee...eeeeee..eeeeeee............eeeeeee.......eeeeeeeee....hhhhhhhhhhhh..................eeeeee.....eeeee......eeeee.....................eeeee.........eeeeeeee..eeeeeeee......eee.eeee......ee..eeee..........eeee..........eeeeeeee....eeeeeeehhhhhhh............eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4kbb A  862 NNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE 1291
                                   871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151|     1168      1178      1188      1198      1208      1218      1228      1238      1254      1264      1274      1284       
                                                                                                                                                                                                                                                                                                                          1151|                                                                                  1245|                                       
                                                                                                                                                                                                                                                                                                                           1159                                                                                   1252

Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kbbb1 B:862-1079 Botulinum neurotoxin                                                                                                                                                                                   d4kbbb2 B:1080-1291 Botulinum neurotoxin                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eee......eeee....ee....eeee.......eeee.............eeeeeeee.......hhhhhhhheeeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee...eeeeee..eeeeeee............eeeeeee.......eeeeeeeee....hhhhhhhhhhhhhh................eeeeee.....eeeee......eeeee.....................eeeee........eeeeeeee..eeeeeeee......eee.eeee......ee..eeee..........eeee..........eeeeeeeee...eeeeeeeehhhhhhh............eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4kbb B  862 NNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE 1291
                                   871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1159      1169      1179      1189      1199      1209      1219      1229      1239      1254      1264      1274      1284       
                                                                                                                                                                                                                                                                                                                         1150|                                                                                   1246|                                       
                                                                                                                                                                                                                                                                                                                          1159                                                                                    1252

Chain C from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                4kbb C   45 DMFAKLKEKFFNEIN   59
                                    54

Chain D from PDB  Type:PROTEIN  Length:18
                                                   
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                4kbb D   42 SQEDMFAKLKEKFFNEIN   59
                                    51

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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 '\|'

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

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

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		Lys B:1270 - Pro B:1271	[ RasMol ]

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Description

Compounds

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Ligands, Modified Residues, Ions (6, 15)

Sites (5, 5)

SS Bonds (0, 0)

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