1VP6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   M.LOTI ION CHANNEL CYLIC NUCLEOTIDE BINDING DOMAIN

Authors :   G. M. Clayton, W. R. Silverman, L. Heginbotham, J. H. Morais-Cabral

Date :   14 Oct 04 (Deposition) - 26 Oct 04 (Release) - 11 Nov 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,C

Keywords :   Dimer Helical Bundle Beta Barrel Core With Cyclic Amp Bound, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. M. Clayton, W. R. Silverman, L. Heginbotham, J. H. Morais-Cabral
Structural Basis Of Ligand Activation In A Cyclic Nucleotide Regulated Potassium Channel.
Cell(Cambridge, Mass. ) V. 119 615 2004
PubMed-ID: 15550244 | Reference-DOI: 10.1016/J.CELL.2004.10.030
(for further references see the PDB file header)

Molecule 1 - CYCLIC-NUCLEOTIDE BINDING DOMAIN OF MESORHIZOBIUM LOTI CNG POTASSIUM CHANNEL
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21-RP
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MESORHIZOBIUM LOTI
	Organism Taxid	:	381
	Synonym	:	CNBD

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 18)

No.	Name	Count	Type	Full Name
1	BR	16	Ligand/Ion	BROMIDE ION
2	CMP	2	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:278	BINDING SITE FOR RESIDUE BR A 356
02	AC2	SOFTWARE	ARG A:252 , ARG A:271 , SER A:321 , HIS A:323 , HOH A:441	BINDING SITE FOR RESIDUE BR A 357
03	AC3	SOFTWARE	ARG A:307 , HOH A:379	BINDING SITE FOR RESIDUE BR A 358
04	AC4	SOFTWARE	HOH A:385	BINDING SITE FOR RESIDUE BR A 361
05	AC5	SOFTWARE	PRO A:234 , ARG A:264 , HOH A:456	BINDING SITE FOR RESIDUE BR A 362
06	AC6	SOFTWARE	ARG A:349	BINDING SITE FOR RESIDUE BR A 363
07	AC7	SOFTWARE	ALA A:231 , HOH A:432 , HOH A:451 , VAL C:224	BINDING SITE FOR RESIDUE BR A 364
08	AC8	SOFTWARE	GLY A:240 , ALA A:242 , VAL A:243	BINDING SITE FOR RESIDUE BR A 365
09	AC9	SOFTWARE	HOH A:439 , HOH C:420	BINDING SITE FOR RESIDUE BR A 366
10	BC1	SOFTWARE	ARG A:249	BINDING SITE FOR RESIDUE BR A 367
11	BC2	SOFTWARE	ARG C:252 , ARG C:271 , SER C:321 , HIS C:323	BINDING SITE FOR RESIDUE BR C 356
12	BC3	SOFTWARE	ARG C:252 , ARG C:254 , ARG C:271 , SER C:321	BINDING SITE FOR RESIDUE BR C 357
13	BC4	SOFTWARE	ILE C:262 , ARG C:307 , HOH C:416	BINDING SITE FOR RESIDUE BR C 358
14	BC5	SOFTWARE	ARG C:349	BINDING SITE FOR RESIDUE BR C 359
15	BC6	SOFTWARE	VAL A:282 , PHE A:296 , GLY A:297 , GLU A:298 , MET A:299 , ALA A:300 , ARG A:307 , SER A:308 , ALA A:309 , VAL A:311 , ARG A:348 , HOH A:375 , HOH A:411 , HOH A:431	BINDING SITE FOR RESIDUE CMP A 368
16	BC7	SOFTWARE	VAL C:282 , PHE C:296 , GLY C:297 , GLU C:298 , MET C:299 , ALA C:300 , ARG C:307 , SER C:308 , ALA C:309 , VAL C:311 , ARG C:348 , HOH C:363 , HOH C:446 , HOH C:468	BINDING SITE FOR RESIDUE CMP C 360

(no "SS Bond" information available for 1VP6)

(no "Cis Peptide Bond" information available for 1VP6)

(no "SAP(SNP)/Variant" information available for 1VP6)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CNGK1_RHILO	235-348	2	A:235-348 C:235-348
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CNGK1_RHILO	262-278	2	A:262-278 C:262-278
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CNGK1_RHILO	296-313	2	A:296-313 C:296-313

(no "Exon" information available for 1VP6)

Asymmetric/Biological 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:133
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:133
                                   227       237       247       257       267       277       287       297       307       317       327       337       347   
          CNGK1_RHILO   218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG 350
               SCOP domains d1vp6a_ A: Putative ion channel CnbD                                                                                                  SCOP domains
               CATH domains 1vp6A00 A:218-350 Jelly Rolls                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eee.....eee....eehhhhhhhh......eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------CNMP_BINDING_3  PDB: A:235-348 UniProt: 235-348                                                                   -- PROSITE (1)
                PROSITE (2) --------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vp6 A 218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG 350
                                   227       237       247       257       267       277       287       297       307       317       327       337       347

Chain C from PDB  Type:PROTEIN  Length:133
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:133
                                   227       237       247       257       267       277       287       297       307       317       327       337       347   
          CNGK1_RHILO   218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG 350
               SCOP domains d1vp6c_ C: Putative ion channel CnbD                                                                                                  SCOP domains
               CATH domains 1vp6C00 C:218-350 Jelly Rolls                                                                                                         CATH domains
           Pfam domains (1) -----------------------------------cNMP_binding-1vp6C01 C:253-336                                                      -------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------cNMP_binding-1vp6C02 C:253-336                                                      -------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eee.....eee....eehhhhhhhh......eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------CNMP_BINDING_3  PDB: C:235-348 UniProt: 235-348                                                                   -- PROSITE (1)
                PROSITE (2) --------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vp6 C 218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG 350
                                   227       237       247       257       267       277       287       297       307       317       327       337       347

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: cAMP-binding domain (78)

Protein domain: Putative ion channel CnbD (2)

Mesorhizobium loti [TaxId: 381] (2)

1a	d1vp6a_	A:
1b	d1vp6c_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Mesorhizobium loti. Organism_taxid: 381. (1)

1a	1vp6A00	A:218-350
1b	1vp6C00	C:218-350

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: cNMP_binding] (41)

Family: cNMP_binding (41)

Rhizobium loti (Mesorhizobium loti) (4)

1a	cNMP_binding-1vp6C01	C:253-336
1b	cNMP_binding-1vp6C02	C:253-336

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (CNGK1_RHILO | Q98GN8)

molecular function
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	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:0005267	potassium channel activity	Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	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: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:0006813	potassium ion transport	The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

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