1I7L - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX OF THE C DOMAIN OF SYNAPSIN II FROM RAT WITH ATP

Authors :   L. Esser, M. Palnitkar, J. Deisenhofer

Date :   09 Mar 01 (Deposition) - 01 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Synapse, Phosphorylation, Synapsin Iia C-Domain, Atp Binding, Neuropeptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Esser, M. Palnitkar, J. Deisenhofer
Atp Binding Independent Of Metal Cations In Synapsin Ii
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SYNAPSIN II
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C DOMAIN (RESIDUES 113-421)
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:248 , LYS A:270 , SER A:276 , GLY A:277 , LYS A:280 , GLU A:306 , PRO A:307 , PHE A:308 , ILE A:309 , ASP A:314 , ARG A:329 , THR A:338 , ASN A:339 , LYS A:374 , VAL A:376 , PHE A:386 , HOH A:1085 , HOH A:1086 , HOH A:1105 , HOH A:1109	BINDING SITE FOR RESIDUE ATP A 800
2	AC2	SOFTWARE	LYS B:226 , ILE B:248 , LYS B:270 , HIS B:275 , SER B:276 , GLY B:277 , LYS B:280 , GLU B:306 , PRO B:307 , ILE B:309 , ASP B:314 , ARG B:329 , TRP B:336 , LYS B:337 , THR B:338 , ASN B:339 , LYS B:374 , PHE B:386 , GLU B:387 , HOH B:1165 , HOH B:1175 , HOH B:1186 , HOH B:1193	BINDING SITE FOR RESIDUE ATP B 801

(no "SS Bond" information available for 1I7L)

Asymmetric Unit

No.	Residues
1	Ile A:214	-	Asn A:215
2	Phe A:265	-	Pro A:266
3	Ile B:214	-	Asn B:215
4	Phe B:265	-	Pro B:266

(no "SAP(SNP)/Variant" information available for 1I7L)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SYNAPSIN_2	PS00416	Synapsins signature 2.	SYN2_RAT	272-282	2	A:272-282 B:272-282

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SYNAPSIN_2	PS00416	Synapsins signature 2.	SYN2_RAT	272-282	2	A:272-282 B:272-282

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SYNAPSIN_2	PS00416	Synapsins signature 2.	SYN2_RAT	272-282	4	A:272-282 B:272-282

(no "Exon" information available for 1I7L)

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:309
 aligned with SYN2_RAT | Q63537 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:309
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412         
             SYN2_RAT   113 KAKVLLVVDEPHTDWAKCFRGKKILGDYDIKVEQAEFSELNLVAHADGTYAVDMQVLRNGTKVVRSFRPDFVLIRQHAFGMAENEDFRHLVIGMQYAGLPSINSLESIYNFCDKPWVFAQMVAIFKTLGGEKFPLIEQTYYPNHREMLTLPTFPVVVKIGHAHSGMGKVKVENHYDFQDIASVVALTQTYATAEPFIDAKYDIRVQKIGNNYKAYMRTSISGNWKTNTGSAMLEQIAMSDRYKLWVDACSEMFGGLDICAVKAVHGKDGKDYIFEVMDCSMPLIGEHQVEDRQLITDLVISKMNQLLSR 421
               SCOP domains d1i7la1 A:113-214 Synapsin II                                                                         d1i7la2 A:215-421 Synapsin II                                                                                                                                                                                   SCOP domains
               CATH domains 1i7lA02 A:113-215,A:395-407  [code=3.40.50.20, no name defined]                                        1i7lA03 A:216-248,A:309-394      1i7lA01 A:249-308 ATP-grasp fold, A domain                  1i7lA03 A:216-248,A:309-394 ATP-grasp fold, B domain                                  1i7lA02      -------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhh..ee...eeeeeeeehhh.eeeeee....eeeeeee......eeeee...eeee............hhhhhhhhhhh...ee.hhhhhhhh.hhhhhhhhhhhhhhhhh.........eee.hhhhhhh.....eeeee........eeee...hhhhhhhhhhhhhh..eeeee...eeeeeeeeee..eeeeeeeee...........eeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee.........hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SYNAPSIN_2 ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i7l A 113 KAKVLLVVDEPHTDWAKCFRGKKILGDYDIKVEQAEFSELNLVAHADGTYAVDMQVLRNGTKVVRSFRPDFVLIRQHAFGMAENEDFRHLVIGMQYAGLPSINSLESIYNFCDKPWVFAQMVAIFKTLGGEKFPLIEQTYYPNHREMLTLPTFPVVVKIGHAHSGMGKVKVENHYDFQDIASVVALTQTYATAEPFIDAKYDIRVQKIGNNYKAYMRTSISGNWKTNTGSAMLEQIAMSDRYKLWVDACSEMFGGLDICAVKAVHGKDGKDYIFEVMDCSMPLIGEHQVEDRQLITDLVISKMNQLLSR 421
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with SYN2_RAT | Q63537 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:309
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412         
             SYN2_RAT   113 KAKVLLVVDEPHTDWAKCFRGKKILGDYDIKVEQAEFSELNLVAHADGTYAVDMQVLRNGTKVVRSFRPDFVLIRQHAFGMAENEDFRHLVIGMQYAGLPSINSLESIYNFCDKPWVFAQMVAIFKTLGGEKFPLIEQTYYPNHREMLTLPTFPVVVKIGHAHSGMGKVKVENHYDFQDIASVVALTQTYATAEPFIDAKYDIRVQKIGNNYKAYMRTSISGNWKTNTGSAMLEQIAMSDRYKLWVDACSEMFGGLDICAVKAVHGKDGKDYIFEVMDCSMPLIGEHQVEDRQLITDLVISKMNQLLSR 421
               SCOP domains d1i7lb1 B:113-214 Synapsin II                                                                         d1i7lb2 B:215-421 Synapsin II                                                                                                                                                                                   SCOP domains
               CATH domains 1i7lB02 B:113-215,B:395-407  [code=3.40.50.20, no name defined]                                        1i7lB03 B:216-248,B:309-394      1i7lB01 B:249-308 ATP-grasp fold, A domain                  1i7lB03 B:216-248,B:309-394 ATP-grasp fold, B domain                                  1i7lB02      -------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhh...ee...eeeeeeeehhh.eeeeee....eeeee.eee..eee..ee...eeee............hhhhhhhhhhh...ee.hhhhhhhh.hhhhhhhhhhhhhhhhh.........eee.hhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhhhh..eeeee...eeeeeeeeee..eeeeeeeee...........eeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SYNAPSIN_2 ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i7l B 113 KAKVLLVVDEPHTDWAKCFRGKKILGDYDIKVEQAEFSELNLVAHADGTYAVDMQVLRNGTKVVRSFRPDFVLIRQHAFGMAENEDFRHLVIGMQYAGLPSINSLESIYNFCDKPWVFAQMVAIFKTLGGEKFPLIEQTYYPNHREMLTLPTFPVVVKIGHAHSGMGKVKVENHYDFQDIASVVALTQTYATAEPFIDAKYDIRVQKIGNNYKAYMRTSISGNWKTNTGSAMLEQIAMSDRYKLWVDACSEMFGGLDICAVKAVHGKDGKDYIFEVMDCSMPLIGEHQVEDRQLITDLVISKMNQLLSR 421
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

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: Alpha and beta proteins (a+b) (23004)

Fold: ATP-grasp (191)

Superfamily: Glutathione synthetase ATP-binding domain-like (158)

Family: Synapsin C-terminal domain (7)

Protein domain: Synapsin II (2)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

1a	d1i7la2	A:215-421
1b	d1i7lb2	B:215-421

Class: Alpha and beta proteins (a/b) (23833)

Fold: PreATP-grasp domain (131)

Superfamily: PreATP-grasp domain (131)

Family: Synapsin domain (6)

Protein domain: Synapsin II (2)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

2a	d1i7la1	A:113-214
2b	d1i7lb1	B:113-214

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-amino Acid Aminotransferase; Chain A, domain 1 (175)

Homologous Superfamily: ATP-grasp fold, B domain (118)

Norway rat (Rattus norvegicus) (4)

1a	1i7lA03	A:216-248,A:309-394
1b	1i7lB03	B:216-248,B:309-394

Topology: Dna Ligase; domain 1 (375)

Homologous Superfamily: ATP-grasp fold, A domain (109)

Norway rat (Rattus norvegicus) (4)

2a	1i7lA01	A:249-308
2b	1i7lB01	B:249-308

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.20, no name defined] (85)

Norway rat (Rattus norvegicus) (4)

3a	1i7lA02	A:113-215,A:395-407
3b	1i7lB02	B:113-215,B:395-407

(no "Pfam Domain" information available for 1I7L)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYN2_RAT | Q63537)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0008092	cytoskeletal protein binding	Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
	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).
biological process
	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.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	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.
	GO:0030672	synaptic vesicle membrane	The lipid bilayer surrounding a synaptic vesicle.
	GO:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:214 - Asn A:215	[ RasMol ]
		Ile B:214 - Asn B:215	[ RasMol ]
		Phe A:265 - Pro A:266	[ RasMol ]
		Phe B:265 - Pro B:266	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1i7l
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SYN2_RAT \| Q63537
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SYN2_RAT \| Q63537
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SYN2_RAT \| Q63537	:	1i7n

1auv	CRYSTAL STRUCTURE OF THE C DOMAIN OF SYNAPSIN I FROM BOVINE BRAIN
1aux	CRYSTAL STRUCTURE OF THE COMPLEX OF THE C DOMANIN OF SYNAPSIN I FROM BOVINE BRAIN WITH ATP-GAMMA-S
1i7n	1I7N CONTAINS THE SAME PROTEIN, WITHOUT ATP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (3, 6)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File