1SY9 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURE OF CALMODULIN COMPLEXED WITH A FRAGMENT OF THE OLFACTORY CNG CHANNEL

Authors :   G. M. Contessa, M. Orsale, S. Melino, V. Torre, M. Paci, A. Desideri, D. O. Cicero

Date :   01 Apr 04 (Deposition) - 12 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   4 Helix-Turn-Helix, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. M. Contessa, M. Orsale, S. Melino, V. Torre, M. Paci, A. Desideri, D. O. Cicero
Structure Of Calmodulin Complexed With An Olfactory Cng Channel Fragment And Role Of The Central Linker: Residual Dipolar Couplings To Evaluate Calmodulin Binding Modes Outside The Kinase Family.
J. Biomol. Nmr V. 31 185 2005
PubMed-ID: 15803393 | Reference-DOI: 10.1007/S10858-005-0165-1
(for further references see the PDB file header)

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

Molecule 2 - CYCLIC-NUCLEOTIDE-GATED OLFACTORY CHANNEL
	Chains	:	B
	Engineered	:	YES
	Fragment	:	RESIDUES 151-176
	Other Details	:	THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN BOS TAURUS (BOVINE).
	Synonym	:	CYCLIC-NUCLEOTIDE-GATED CATION CHANNEL 2, CNG CHANNEL 2, CNG-2, CNG2
	Synthetic	:	YES


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

NMR Structure (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31	BINDING SITE FOR RESIDUE CA A 149
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67	BINDING SITE FOR RESIDUE CA A 150
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104	BINDING SITE FOR RESIDUE CA A 151
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140	BINDING SITE FOR RESIDUE CA A 152

(no "SS Bond" information available for 1SY9)

(no "Cis Peptide Bond" information available for 1SY9)

(no "SAP(SNP)/Variant" information available for 1SY9)

NMR Structure (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CAM2B_XENLA	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CAM2A_XENLA	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CALM1_XENLA	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CAM2B_XENLA	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CAM2A_XENLA	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM1_XENLA	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 1SY9)

NMR Structure

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:148
 aligned with CALM1_XENLA | P0DP33 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          CALM1_XENLA     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains ---d1sy9a1 A:4-148 Calmodulin                                                                                                                        SCOP domains
               CATH domains 1sy9A00 A:1-148 EF-hand                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (5)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sy9 A   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with CAM2A_XENLA | P0DP34 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          CAM2A_XENLA     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains ---d1sy9a1 A:4-148 Calmodulin                                                                                                                        SCOP domains
               CATH domains 1sy9A00 A:1-148 EF-hand                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sy9 A   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with CAM2B_XENLA | P0DP35 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          CAM2B_XENLA     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains ---d1sy9a1 A:4-148 Calmodulin                                                                                                                        SCOP domains
               CATH domains 1sy9A00 A:1-148 EF-hand                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (6)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sy9 A   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:19
 aligned with CNGA2_BOVIN | Q03041 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:19
                                    73         
          CNGA2_BOVIN    64 GGFRRIARLVGVLREWAYR  82
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 1sy9 B 155 GGFRRIARLVGVLREWAYR 173
                                   164

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Calmodulin (152)

African clawed frog (Xenopus laevis) [TaxId: 8355] (13)

d1sy9a1

A:4-148

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

African clawed frog (Xenopus laevis) (12)

1sy9A00

A:1-148

(no "Pfam Domain" information available for 1SY9)

NMR Structure(hide GO term definitions)

Chain A (CAM2A_XENLA | P0DP34)

Chain A (CALM1_XENLA | P0DP33)

Chain A (CAM2B_XENLA | P0DP35)

Chain B (CNGA2_BOVIN | Q03041)

molecular function
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0030553	cGMP binding	Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0005222	intracellular cAMP activated cation channel activity	Enables the transmembrane transfer of a cation by a channel that opens when intracellular cAMP has been bound by the channel complex or one of its constituent parts.
	GO:0005223	intracellular cGMP activated cation channel activity	Enables the transmembrane transfer of a cation by a channel that opens when intracellular cGMP has been bound by the channel complex or one of its constituent parts.
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005249	voltage-gated potassium channel activity	Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0098655	cation transmembrane transport	A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071805	potassium ion transmembrane transport	A process in which a potassium ion is transported from one side of a membrane to the other.
	GO:0042391	regulation of membrane potential	Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007608	sensory perception of smell	The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

NMR Structure
	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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sy9)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - model 1, sites PNG format \| NMR Structure - all models 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
	1sy9
		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
	CALM1_XENLA \| P0DP33
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	CAM2A_XENLA \| P0DP34
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	CAM2B_XENLA \| P0DP35
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	CNGA2_BOVIN \| Q03041
		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
	CALM1_XENLA \| P0DP33
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CAM2A_XENLA \| P0DP34
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CAM2B_XENLA \| P0DP35
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CNGA2_BOVIN \| Q03041
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1SY9)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (24, 24)

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