5KJ8 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE CA2+-BOUND SYNAPTOTAGMIN-1 SNARE COMPLEX (LONG UNIT CELL FORM) - FROM SYNCHROTRON DIFFRACTION

Authors :   A. Y. Lyubimov, M. Uervirojnangkoorn, Q. Zhou, M. Zhao, N. K. Sauter, A. S. Brewster, W. I. Weis, A. T. Brunger

Date :   17 Jun 16 (Deposition) - 19 Oct 16 (Release) - 26 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.10

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K
Biol. Unit 1: A,B,C,D,E  (1x)
Biol. Unit 2: F  (1x)
Biol. Unit 3: G,H,I,J,K  (1x)

Keywords :   Xfel Structure, Synaptic Fusion Complex, Synaptotagmin1, Neuronal Snare Complex, Endocytosis, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Y. Lyubimov, M. Uervirojnangkoorn, O. B. Zeldin, Q. Zhou, M. Zhao, A. S. Brewster, T. Michels-Clark, J. M. Holton, N. K. Sauter, W. I. Weis A. T. Brunger
Advances In X-Ray Free Electron Laser (Xfel) Diffraction Data Processing Applied To The Crystal Structure Of The Synaptotagmin-1 / Snare Complex.
Elife V. 5 2016
PubMed-ID: 27731796 | Reference-DOI: 10.7554/ELIFE.18740

Molecule 1 - VESICLE-ASSOCIATED MEMBRANE PROTEIN 3
	Chains	:	A, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 14-76
	Gene	:	VAMP3, SYB3
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	VAMP-3,CELLUBREVIN,CEB,SYNAPTOBREVIN-3

Molecule 2 - SYNTAXIN-1A
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 191-256
	Gene	:	STX1A, SAP
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	NEURON-SPECIFIC ANTIGEN HPC-1,SYNAPTOTAGMIN-ASSOCIATED 35 KDA PROTEIN,P35A

Molecule 3 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
	Chains	:	C, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 9-83
	Gene	:	SNAP25, SNAP
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN

Molecule 4 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
	Chains	:	D, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 141-204
	Gene	:	SNAP25, SNAP
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN

Molecule 5 - SYNAPTOTAGMIN-1
	Chains	:	E, F, K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 141-419
	Gene	:	SYT1
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	SYNAPTOTAGMIN I,SYTI,P65

		1	2	3	4	5	6	7	8	9	10	11
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K
Biological Unit 1 (1x)	:	A	B	C	D	E
Biological Unit 2 (1x)	:						F
Biological Unit 3 (1x)	:							G	H	I	J	K

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 14)

No.	Name	Count	Type	Full Name
1	CA	14	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP C:58	binding site for residue CA C 102
02	AC2	SOFTWARE	ASP E:303 , ASP E:309 , ASP E:363 , TYR E:364 , ASP E:365 , CA E:502	binding site for residue CA E 501
03	AC3	SOFTWARE	MET E:302 , ASP E:303 , ASP E:363 , ASP E:365 , CA E:501	binding site for residue CA E 502
04	AC4	SOFTWARE	ASP E:172 , ASP E:230 , PHE E:231 , ASP E:232 , CA E:504	binding site for residue CA E 503
05	AC5	SOFTWARE	ASP E:172 , ASP E:178 , ASP E:230 , PHE E:231 , CA E:503	binding site for residue CA E 504
06	AC6	SOFTWARE	ASP F:172 , ASP F:178 , ASP F:230 , PHE F:231 , CA F:504	binding site for residue CA F 501
07	AC7	SOFTWARE	ASP F:172 , ASP F:230 , ASP F:232 , LYS F:324	binding site for residue CA F 502
08	AC8	SOFTWARE	ASP F:303 , ASP F:309 , ASP F:363 , TYR F:364	binding site for residue CA F 503
09	AC9	SOFTWARE	ASP F:172 , THR F:176 , SER F:177 , ASP F:178 , CA F:501	binding site for residue CA F 504
10	AD1	SOFTWARE	MET K:302 , ASP K:303 , LEU K:307 , SER K:308 , ASP K:363	binding site for residue CA K 501
11	AD2	SOFTWARE	ASP K:303 , ASP K:309 , ASP K:363 , TYR K:364 , ASP K:365	binding site for residue CA K 502
12	AD3	SOFTWARE	ASP K:172 , ASP K:230 , PHE K:231 , ASP K:232 , CA K:504	binding site for residue CA K 503
13	AD4	SOFTWARE	GLU E:346 , ASP K:172 , ASP K:178 , PHE K:231 , CA K:503	binding site for residue CA K 504

(no "SS Bond" information available for 5KJ8)

Asymmetric Unit

No.	Residues
1	Leu E:171	-	Asp E:172
2	Leu E:186	-	Pro E:187
3	Met F:173	-	Gly F:174
4	Gly F:174	-	Gly F:175
5	Leu F:186	-	Pro F:187
6	Leu K:186	-	Pro K:187
7	Glu K:269	-	Gln K:270

(no "SAP(SNP)/Variant" information available for 5KJ8)

(no "PROSITE Motif" information available for 5KJ8)

(no "Exon" information available for 5KJ8)

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:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5kj8 A  27 GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW  89
                                    36        46        56        66        76        86

Chain B from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5kj8 B 191 ALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVK 256
                                   200       210       220       230       240       250

Chain C from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5kj8 C   9 NELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG  82
                                    18        28        38        48        58        68        78

Chain D from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5kj8 D 142 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG 204
                                   151       161       171       181       191       201

Chain E from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeeee......ee..........eeeeeeee..hhhhhh..eeeeeeee........eeeeeeee.hhh.....eeeeee.............eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee....hhhh.eeeeeeee........eeeeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kj8 E 141 KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV 419
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

Chain F from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeeee......ee..........eeeeeeee..hhhhhh..eeeeeeee........eeeeeeee.hhh.....eeeeee...........eeeeeeeee....eeeeeeeeee..........eeeeeeeee..eeeeeee..........eeeeeeeee....hhhh.eeeeeeee........eeeeeeee....hhhhhhhhhhhhh....eeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kj8 F 141 KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQLGDICFSLRYVPTAGKLTVVILEAKNLKKMDGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV 419
                                   150       160       170       180       190       200       210       220       230       240       250       260       270|      282       292       302||     314       324       334       344       354       364       374       384       394       404       414     
                                                                                                                                                           270|                           303|                                                                                                                 
                                                                                                                                                            273                            306

Chain G from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5kj8 G  27 GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW  89
                                    36        46        56        66        76        86

Chain H from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 5kj8 H 191 ALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAV 255
                                   200       210       220       230       240       250

Chain I from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5kj8 I  10 ELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLGK  83
                                    19        29        39        49        59        69        79

Chain J from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5kj8 J 141 ARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML 203
                                   150       160       170       180       190       200

Chain K from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeee.............eeeeeeee......ee..........eeeeeeee.....hhhh.eeeeeeee........eeeeeeee.........eeeeee.............eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee....hhhh.eeeeeeee........eeeeeeee....hhhhhhhhhhhhh....eeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kj8 K 141 KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV 419
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

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 5KJ8)

(no "CATH Domain" information available for 5KJ8)

(no "Pfam Domain" information available for 5KJ8)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu K:269 - Gln K:270	[ RasMol ]
		Gly F:174 - Gly F:175	[ RasMol ]
		Leu E:171 - Asp E:172	[ RasMol ]
		Leu E:186 - Pro E:187	[ RasMol ]
		Leu F:186 - Pro F:187	[ RasMol ]
		Leu K:186 - Pro K:187	[ RasMol ]
		Met F:173 - Gly F:174	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 14)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (129, 191)

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