4BY5 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DROSOPHILA FRQ2

Authors :   S. Banos-Mateos, A. Chaves-Sanjuan, M. J. Sanchez-Barrena

Date :   17 Jul 13 (Deposition) - 13 Aug 14 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.22

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x),C (1x)
Biol. Unit 2: A (1x),C (1x)
Biol. Unit 3: B,D  (1x)

Keywords :   Calcium-Binding Protein, Calcium Sensor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Romero-Pozuelo, J. S. Dason, A. Mansilla, S. Banos-Mateos, J. L. Sardina, A. Chaves-Sanjuan, J. Jurado-Gomez, E. Santana, H. L. Atwood, A. Hernandez-Hernandez, M. Sanchez-Barrena, A. Ferrus
The Guanine-Exchange Factor Ric8A Binds The Calcium Sensor Ncs-1 To Regulate Synapse Number And Probability Of Release.
J. Cell. Sci. V. 127 4246 2014
PubMed-ID: 25074811 | Reference-DOI: 10.1242/JCS.152603

Molecule 1 - FI18190P1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Other Details	:	CALCIUM BINDING TO EF HANDS 2,3 AND 4
	Synonym	:	FREQUENIN, FREQUENIN 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	CA	12	Ligand/Ion	CALCIUM ION
2	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:73 , ASN A:75 , ASP A:77 , ALA A:79 , GLU A:84 , HOH A:2069	BINDING SITE FOR RESIDUE CA A1183
02	AC2	SOFTWARE	ASP A:109 , ASP A:111 , ASP A:113 , TYR A:115 , GLU A:120 , HOH A:2081	BINDING SITE FOR RESIDUE CA A1184
03	AC3	SOFTWARE	ASP A:156 , ASN A:158 , ASP A:160 , ARG A:162 , GLU A:167 , HOH A:2093	BINDING SITE FOR RESIDUE CA A1185
04	AC4	SOFTWARE	ASP B:73 , ASN B:75 , ASP B:77 , ALA B:79 , GLU B:84 , HOH B:2029	BINDING SITE FOR RESIDUE CA B1185
05	AC5	SOFTWARE	ASP B:156 , ASN B:158 , ASP B:160 , ARG B:162 , GLU B:167 , HOH B:2055	BINDING SITE FOR RESIDUE CA B1186
06	AC6	SOFTWARE	ASP C:73 , ASN C:75 , ASP C:77 , ALA C:79 , GLU C:84 , HOH C:2020	BINDING SITE FOR RESIDUE CA C1185
07	AC7	SOFTWARE	ASP C:109 , ASP C:111 , ASP C:113 , TYR C:115 , GLU C:120 , HOH C:2033	BINDING SITE FOR RESIDUE CA C1186
08	AC8	SOFTWARE	ASP C:156 , ASN C:158 , ASP C:160 , ARG C:162 , GLU C:167 , HOH C:2036	BINDING SITE FOR RESIDUE CA C1187
09	AC9	SOFTWARE	ASP D:73 , ASN D:75 , ASP D:77 , ALA D:79 , GLU D:84 , HOH D:2005	BINDING SITE FOR RESIDUE CA D1183
10	BC1	SOFTWARE	ASP D:156 , ASN D:158 , ASP D:160 , ARG D:162 , GLU D:167 , HOH D:2017	BINDING SITE FOR RESIDUE CA D1184
11	BC2	SOFTWARE	ASP D:109 , ASP D:111 , ASP D:113 , TYR D:115 , GLU D:120	BINDING SITE FOR RESIDUE CA D1185
12	BC3	SOFTWARE	ASP B:109 , ASP B:111 , ASP B:113 , TYR B:115 , GLU B:120 , HOH B:2043	BINDING SITE FOR RESIDUE CA B1187
13	BC4	SOFTWARE	ARG B:70 , ASP B:73 , ASN B:76 , HOH B:2021 , HOH B:2022 , HOH B:2026	BINDING SITE FOR RESIDUE NA B1188

(no "SS Bond" information available for 4BY5)

(no "Cis Peptide Bond" information available for 4BY5)

(no "SAP(SNP)/Variant" information available for 4BY5)

(no "PROSITE Motif" information available for 4BY5)

(no "Exon" information available for 4BY5)

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:171
 aligned with Q9VWX8_DROME | Q9VWX8 from UniProtKB/TrEMBL  Length:187

    Alignment length:178
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174        
         Q9VWX8_DROME     5 NSKLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVGQQPQTEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRIVQAL 182
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhh..-------.hhhhhhhhhhhhhh.....eehhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4by5 A   5 NSKLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVGQ-------NTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRMVQAL 182
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174        
                                                                                                                                                           134     142

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with Q9VWX8_DROME | Q9VWX8 from UniProtKB/TrEMBL  Length:187

    Alignment length:180
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184
         Q9VWX8_DROME     5 NSKLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVGQQPQTEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRIVQALSL 184
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4by5 B   5 NSKLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVGQQPQTEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRMVQALSL 184
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with Q9VWX8_DROME | Q9VWX8 from UniProtKB/TrEMBL  Length:187

    Alignment length:178
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176        
         Q9VWX8_DROME     7 KLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVGQQPQTEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRIVQALSL 184
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh---------hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4by5 C   7 KLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVG---------TPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRMVQALSL 184
                                    16        26        36        46        56        66        76        86        96       106       116       126      |  -      |146       156       166       176        
                                                                                                                                                        133       143

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with Q9VWX8_DROME | Q9VWX8 from UniProtKB/TrEMBL  Length:187

    Alignment length:176
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      
         Q9VWX8_DROME     7 KLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMVGQQPQTEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRIVQAL 182
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhh-----------hhhhhhhhhhhhh.....eehhhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4by5 D   7 KLKQDTIDRLTTDTYFTEKEIRQWHKGFLKDCPNGLLTEQGFIKIYKQFFPDGDPSKFASLVFRVFDENNDGAIEFEEFIRALSITSRGNLDEKLHWAFRLYDVDNDGYITREEMYNIVDAIYQMV-----------PQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRMVQAL 182
                                    16        26        36        46        56        66        76        86        96       106       116       126     |   -       146       156       166       176      
                                                                                                                                                       132         144

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 4BY5)

(no "CATH Domain" information available for 4BY5)

(no "Pfam Domain" information available for 4BY5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9VWX8_DROME | Q9VWX8)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007268	chemical synaptic transmission	The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
	GO:0007528	neuromuscular junction development	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
	GO:0007269	neurotransmitter secretion	The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
	GO:0046928	regulation of neurotransmitter secretion	Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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4by4	CRYSTAL STRUCTURE OF DROSOPHILA FRQ2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (8, 8)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File