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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A C2 DOMAIN FROM HUMAN SYNAPTOTAGMIN-LIKE PROTEIN 4

Authors :   J. B. Bonanno, M. Rutter, K. T. Bain, S. Miller, R. Romero, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   26 Nov 08 (Deposition) - 23 Dec 08 (Release) - 23 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Structural Genomics, Phospholipid Binding, Alternative Splicing, Cell Membrane, Cytoplasmic Vesicle, Membrane, Metal-Binding, Phosphoprotein, Polymorphism, Zinc, Zinc- Finger, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Bonanno, M. Rutter, K. T. Bain, S. Miller, R. Romero, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A C2 Domain From Human Synaptotagmin-Like Protein 4
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SYNAPTOTAGMIN-LIKE PROTEIN 4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET26
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C2 DOMAIN
	Gene	:	SYTL4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EXOPHILIN-2, GRANUPHILIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3FDW)

(no "Site" information available for 3FDW)

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

Asymmetric Unit

No.	Residues
1	Leu A:402	-	Pro A:403
2	Leu B:402	-	Pro B:403

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016076	I	420	V	SYTL4_HUMAN	Polymorphism	2022039	A/B	V	420	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016076	I	420	V	SYTL4_HUMAN	Polymorphism	2022039	A	V	420	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016076	I	420	V	SYTL4_HUMAN	Polymorphism	2022039	B	V	420	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	SYTL4_HUMAN	372-462 527-617	2	A:372-462 B:372-462 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	SYTL4_HUMAN	372-462 527-617	1	A:372-462 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	SYTL4_HUMAN	372-462 527-617	1	- B:372-462 -

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000372989	2b	ENSE00001459253	X:99986498-99986406	93	SYTL4_HUMAN	-	0	0	-	-
1.3a	ENST00000372989	3a	ENSE00001459251	X:99959882-99959807	76	SYTL4_HUMAN	-	0	0	-	-
1.4	ENST00000372989	4	ENSE00001796780	X:99958181-99958089	93	SYTL4_HUMAN	-	0	0	-	-
1.5b	ENST00000372989	5b	ENSE00001382017	X:99957103-99956924	180	SYTL4_HUMAN	1-37	37	0	-	-
1.6	ENST00000372989	6	ENSE00001154545	X:99956669-99956454	216	SYTL4_HUMAN	37-109	73	0	-	-
1.7	ENST00000372989	7	ENSE00001154536	X:99956325-99956216	110	SYTL4_HUMAN	109-146	38	0	-	-
1.8	ENST00000372989	8	ENSE00001154529	X:99955995-99955893	103	SYTL4_HUMAN	146-180	35	0	-	-
1.9	ENST00000372989	9	ENSE00001304452	X:99946206-99946105	102	SYTL4_HUMAN	180-214	35	0	-	-
1.10	ENST00000372989	10	ENSE00000673591	X:99945635-99945560	76	SYTL4_HUMAN	214-239	26	0	-	-
1.11	ENST00000372989	11	ENSE00000673572	X:99945162-99945072	91	SYTL4_HUMAN	240-270	31	0	-	-
1.12	ENST00000372989	12	ENSE00000673564	X:99944956-99944853	104	SYTL4_HUMAN	270-304	35	0	-	-
1.13a	ENST00000372989	13a	ENSE00000673560	X:99943440-99943348	93	SYTL4_HUMAN	305-335	31	0	-	-
1.13d	ENST00000372989	13d	ENSE00000673548	X:99942242-99942064	179	SYTL4_HUMAN	336-395	60	2	A:354-395 B:354-395	42 42
1.13e	ENST00000372989	13e	ENSE00000673528	X:99941778-99941676	103	SYTL4_HUMAN	395-429	35	2	A:395-429 B:395-429	35 35
1.13f	ENST00000372989	13f	ENSE00001218079	X:99941148-99940987	162	SYTL4_HUMAN	430-483	54	2	A:430-483 B:430-483	54 54
1.14	ENST00000372989	14	ENSE00001217979	X:99936332-99936224	109	SYTL4_HUMAN	484-520	37	0	-	-
1.15	ENST00000372989	15	ENSE00001217969	X:99934409-99934310	100	SYTL4_HUMAN	520-553	34	0	-	-
1.16b	ENST00000372989	16b	ENSE00000673492	X:99933596-99933388	209	SYTL4_HUMAN	553-623	71	0	-	-
1.17c	ENST00000372989	17c	ENSE00001459238	X:99931173-99929488	1686	SYTL4_HUMAN	623-671	49	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:130
 aligned with SYTL4_HUMAN | Q96C24 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:130
                                   363       373       383       393       403       413       423       433       443       453       463       473       483
          SYTL4_HUMAN   354 IFVTGRIAFSLKYEQQTQSLVVHVKECHQLAYADEAKKRSNPYVKTYLLPDKSRQGKRKTSIKRDTINPLYDETLRYEIPESLLAQRTLQFSVWHHGRFGRNTFLGEAEIQMDSWKLDKKLDHCLPLHGK 483
               SCOP domains d3fdwa_ A: automated matches                                                                                                       SCOP domains
               CATH domains 3fdwA00 A:354-483 C2- domain Calcium/lipid binding domain                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee.............eeeeeeee...hhh.eee..........eeeeeeeee....hhhh.eeeeeeeee.hhh.eeeeeeeeeehhhhh.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------V--------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------C2  PDB: A:372-462 UniProt: 372-462                                                        --------------------- PROSITE
           Transcript 1 (1) Exon 1.13d  PDB: A:354-395 [INCOMPLETE]   ----------------------------------Exon 1.13f  PDB: A:430-483 UniProt: 430-483            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.13e  PDB: A:395-429         ------------------------------------------------------ Transcript 1 (2)
                 3fdw A 354 IFVTGRIAFSLKYEQQTQSLVVHVKECHQLAYADEAKKRSNPYVKTYLLPDKSRQGKRKTSIKRDTVNPLYDETLRYEIPESLLAQRTLQFSVWHHGRFGRNTFLGEAEIQMDSWKLDKKLDHCLPLHGK 483
                                   363       373       383       393       403       413       423       433       443       453       463       473       483

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with SYTL4_HUMAN | Q96C24 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:130
                                   363       373       383       393       403       413       423       433       443       453       463       473       483
          SYTL4_HUMAN   354 IFVTGRIAFSLKYEQQTQSLVVHVKECHQLAYADEAKKRSNPYVKTYLLPDKSRQGKRKTSIKRDTINPLYDETLRYEIPESLLAQRTLQFSVWHHGRFGRNTFLGEAEIQMDSWKLDKKLDHCLPLHGK 483
               SCOP domains d3fdwb_ B: automated matches                                                                                                       SCOP domains
               CATH domains 3fdwB00 B:354-483 C2- domain Calcium/lipid binding domain                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee.............eeeeeeee...hhh.eee..........eeeeeeeee.hhhhhh..eeeeeeeee.hhh.eeeeeeeeeehhhhh.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------V--------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------C2  PDB: B:372-462 UniProt: 372-462                                                        --------------------- PROSITE
           Transcript 1 (1) Exon 1.13d  PDB: B:354-395 [INCOMPLETE]   ----------------------------------Exon 1.13f  PDB: B:430-483 UniProt: 430-483            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.13e  PDB: B:395-429         ------------------------------------------------------ Transcript 1 (2)
                 3fdw B 354 IFVTGRIAFSLKYEQQTQSLVVHVKECHQLAYADEAKKRSNPYVKTYLLPDKSRQGKRKTSIKRDTVNPLYDETLRYEIPESLLAQRTLQFSVWHHGRFGRNTFLGEAEIQMDSWKLDKKLDHCLPLHGK 483
                                   363       373       383       393       403       413       423       433       443       453       463       473       483

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: C2 domain (Calcium/lipid-binding domain, CaLB) (148)

Family: automated matches (29)

Protein domain: automated matches (29)

Human (Homo sapiens) [TaxId: 9606] (18)

1a	d3fdwa_	A:
1b	d3fdwb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: C2- domain Calcium/lipid binding domain (78)

Human (Homo sapiens) (41)

1a	3fdwA00	A:354-483
1b	3fdwB00	B:354-483

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYTL4_HUMAN | Q96C24)

molecular function
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005544	calcium-dependent phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
	GO:0030276	clathrin binding	Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042043	neurexin family protein binding	Interacting selectively and non-covalently with neurexins, synaptic cell surface proteins related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals.
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019905	syntaxin binding	Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
biological process
	GO:0048791	calcium ion-regulated exocytosis of neurotransmitter	The release of a neurotransmitter into the synaptic cleft by exocytosis of synaptic vesicles, where the release step is dependent on a rise in cytosolic calcium ion levels.
	GO:0006887	exocytosis	A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0071985	multivesicular body sorting pathway	A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded.
	GO:0046676	negative regulation of insulin secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.
	GO:0045921	positive regulation of exocytosis	Any process that activates or increases the frequency, rate or extent of exocytosis.
	GO:0050714	positive regulation of protein secretion	Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
	GO:0017158	regulation of calcium ion-dependent exocytosis	Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis.
	GO:0006906	vesicle fusion	Fusion of the membrane of a transport vesicle with its target membrane.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070382	exocytic vesicle	A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.
	GO:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0098793	presynapse	The part of a synapse that is part of the presynaptic cell.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
	GO:0030667	secretory granule membrane	The lipid bilayer surrounding a secretory granule.
	GO:0030658	transport vesicle membrane	The lipid bilayer surrounding a transport vesicle.

Asymmetric Unit
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(no "Sites" information available for 3fdw)

	Cis Peptide Bonds
		Leu A:402 - Pro A:403	[ RasMol ]
		Leu B:402 - Pro B:403	[ RasMol ]

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