5JLV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   RECEPTOR BINDING DOMAIN OF BOTULINUM NEUROTOXIN A IN COMPLEX WITH HUMAN GLYCOSYLATED SV2C

Authors :   G. Yao, S. Zhang, S. Mahrhold, K. Lam, D. Stern, K. Bagramyan, K. Perry, M A. Rummel, M. Dong, R. Jin

Date :   27 Apr 16 (Deposition) - 15 Jun 16 (Release) - 03 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Glycosylation, Botulinum Neurotoxin, Receptor Binding Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Yao, S. Zhang, S. Mahrhold, K. H. Lam, D. Stern, K. Bagramyan, K. Perry, M. Kalkum, A. Rummel, M. Dong, R. Jin
N-Linked Glycosylation Of Sv2 Is Required For Binding And Uptake Of Botulinum Neurotoxin A.
Nat. Struct. Mol. Biol. V. 23 656 2016
PubMed-ID: 27294781 | Reference-DOI: 10.1038/NSMB.3245

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A
	Chains	:	A, B
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 872-1296
	Gene	:	BOTA, ATX, BNA
	Mutation	:	YES
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM
	Organism Taxid	:	1491
	Synonym	:	BONT/A,BONTOXILYSIN-A,BOTOX

Molecule 2 - SYNAPTIC VESICLE GLYCOPROTEIN 2C
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	MAMMALIAN EXPRESSION VECTOR PCBIO
	Expression System Taxid	:	386595
	Fragment	:	UNP RESIDUES 473-567
	Gene	:	SV2C, KIAA1054
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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 (5, 14)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
4	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (5, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:1009 , ARG A:1013 , ASN A:1032 , ASN A:1233 , HOH A:1551 , HOH A:1562	binding site for residue ACT A 1301
2	AC2	SOFTWARE	LYS A:1028 , LEU A:1035 , GLN A:1038 , HOH A:1448 , HOH A:1537	binding site for residue PO4 A 1302
3	AC3	SOFTWARE	GLU A:982 , ARG A:996 , LYS A:1000 , HOH A:1419 , HOH A:1436 , HOH A:1590	binding site for residue PO4 A 1303
4	AC4	SOFTWARE	ARG B:1276 , GLU C:470 , GLY C:471 , ARG C:472	binding site for residue ACT B 1301
5	AC5	SOFTWARE	MET B:1144	binding site for residue ACT B 1302
6	AC6	SOFTWARE	GLU B:982 , ARG B:996 , VAL B:998	binding site for residue PO4 B 1303
7	AC7	SOFTWARE	ASP C:514 , ASN C:534 , HOH C:706	binding site for Mono-Saccharide NAG C 605 bound to ASN C 534
8	AC8	SOFTWARE	PHE A:953 , HIS A:1064 , GLY A:1292 , HOH A:1445 , HOH A:1476 , HOH A:1484 , ILE C:538 , LYS C:558 , ASN C:559 , HOH C:701 , HOH C:711 , HOH C:712 , HOH C:739 , HOH C:744	binding site for Poly-Saccharide residues FUC C 601 through BMA C 604 bound to ASN C 559
9	AC9	SOFTWARE	HIS B:1064 , ASP B:1289 , GLY B:1292 , HOH B:1433 , HOH B:1485 , ILE D:538 , ASP D:539 , LYS D:558 , ASN D:559 , HOH D:701 , HOH D:705 , HOH D:709	binding site for Poly-Saccharide residues FUC D 601 through NAG D 603 bound to ASN D 559

(no "SS Bond" information available for 5JLV)

Asymmetric Unit

No.	Residues
1	Gly A:1138	-	Pro A:1139
2	Gly B:1138	-	Pro B:1139

(no "SAP(SNP)/Variant" information available for 5JLV)

(no "PROSITE Motif" information available for 5JLV)

(no "Exon" information available for 5JLV)

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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeee..eeee......eeee....eee..eeeeeeee......eeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhh...................eeeee......eeee........eeee....eeee...eeee......eeeeee............eeeeeeee..eeeeee.........ee.eeehhhhh.....eeeeee.........eeeeee.....eeeeeeeeee..eeeeeee.hhhhh...hhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jlv A  870 PMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYANKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL 1296
                                   879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291     
                                                                                                                                                                                                                                                                                                                                 1166|                                                                                                                               
                                                                                                                                                                                                                                                                                                                                  1169

Chain B from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeee..eeee......eeee...eee.......eeee......eeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhhh..................eeee......eeee........eeee....eeee...eeee......eeeeee............eeeeeeee..eeeeee.........ee.eeehhhhh.....eeeeee.........eeeeee.....eeeeeeeeee..eeeeeee.........hhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jlv B  870 PMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYANKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL 1296
                                   879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291     
                                                                                                                                                                                                                                                                                                                                 1166|                                                                                                                               
                                                                                                                                                                                                                                                                                                                                  1169

Chain C from PDB  Type:PROTEIN  Length:97
                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeee...eeeeeee..eeeeeeee..eeeeeeee..eee..eee..eee..eee..eee..eee....hhh.ee..eee.eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                5jlv C  470 EGRVERDKYANFTINFTMENQIHTGMEYDNGRFIGVKFKSVTFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFKNCSFFHNK  566
                                   479       489       499       509       519       529       539       549       559

Chain D from PDB  Type:PROTEIN  Length:91
                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee..eeeeeeee..eeeeeeee..eee..eeeeeeee..eee..eee..eeeee..hhh.ee..eee.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                5jlv D  474 ERDKYANFTINFTMENQIHTGMEYDNGRFIGVKFKSVTFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFKNCSFFH  564
                                   483       493       503       513       523       533       543       553       563

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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 "SCOP Domain" information available for 5JLV)

(no "CATH Domain" information available for 5JLV)

(no "Pfam Domain" information available for 5JLV)

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	Cis Peptide Bonds
		Gly A:1138 - Pro A:1139	[ RasMol ]
		Gly B:1138 - Pro B:1139	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 5JLV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (33, 35)

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