1G4Y - JenaLib

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Title :   1.60 A CRYSTAL STRUCTURE OF THE GATING DOMAIN FROM SMALL CONDUCTANCE POTASSIUM CHANNEL COMPLEXED WITH CALCIUM-CALMODULIN

Authors :   M. A. Schumacher, A. Rivard, H. P. Bachinger, J. P. Adelman

Date :   07 Jan 01 (Deposition) - 09 May 01 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Small-Conductance Calcium-Activated Potassium Channel, Calmodulin, Calmodulin Binding Domain (Cambd), Channel Gating, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Schumacher, A. F. Rivard, H. P. Bachinger, J. P. Adelman
Structure Of The Gating Domain Of A Ca2+-Activated K+ Channel Complexed With Ca2+/Calmodulin.
Nature V. 410 1120 2001
PubMed-ID: 11323678 | Reference-DOI: 10.1038/35074145

Molecule 1 - CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET23B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CALMODULIN-BINDING DOMAIN
	Gene	:	RAT
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 2 - CALMODULIN
	Chains	:	R
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET33B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RAT
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP R:20 , ASP R:22 , ASP R:24 , THR R:26 , GLU R:31 , HOH R:1024	BINDING SITE FOR RESIDUE CA R 1001
2	AC2	SOFTWARE	ASP R:56 , ALA R:57 , ASP R:58 , ASN R:60 , THR R:62 , GLU R:67	BINDING SITE FOR RESIDUE CA R 1002
3	AC3	SOFTWARE	ARG B:429 , LYS B:451 , HIS B:452 , LYS B:455	BINDING SITE FOR RESIDUE SO4 B 799

(no "SS Bond" information available for 1G4Y)

(no "Cis Peptide Bond" information available for 1G4Y)

(no "SAP(SNP)/Variant" information available for 1G4Y)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM3_RAT	8-43 44-79 81-116 117-149	4	R:7-42 R:43-78 R:80-115 R:116-147
				CALM1_RAT	8-43 44-79 81-116 117-149	4	R:7-42 R:43-78 R:80-115 R:116-147
				CALM2_RAT	8-43 44-79 81-116 117-149	4	R:7-42 R:43-78 R:80-115 R:116-147
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM3_RAT	21-33 57-69 94-106 130-142	4	R:20-32 R:56-68 R:93-105 R:129-141
				CALM1_RAT	21-33 57-69 94-106 130-142	4	R:20-32 R:56-68 R:93-105 R:129-141
				CALM2_RAT	21-33 57-69 94-106 130-142	4	R:20-32 R:56-68 R:93-105 R:129-141

Biological Unit 1 (2, 48)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM3_RAT	8-43 44-79 81-116 117-149	8	R:7-42 R:43-78 R:80-115 R:116-147
				CALM1_RAT	8-43 44-79 81-116 117-149	8	R:7-42 R:43-78 R:80-115 R:116-147
				CALM2_RAT	8-43 44-79 81-116 117-149	8	R:7-42 R:43-78 R:80-115 R:116-147
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM3_RAT	21-33 57-69 94-106 130-142	8	R:20-32 R:56-68 R:93-105 R:129-141
				CALM1_RAT	21-33 57-69 94-106 130-142	8	R:20-32 R:56-68 R:93-105 R:129-141
				CALM2_RAT	21-33 57-69 94-106 130-142	8	R:20-32 R:56-68 R:93-105 R:129-141

Asymmetric Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENSRNOT00000022530	1b	ENSRNOE00000159150	chr18:39560962-39561450	489	KCNN2_RAT	1-163	163	0	-	-
1.2	ENSRNOT00000022530	2	ENSRNOE00000159353	chr18:39562034-39562129	96	KCNN2_RAT	164-195	32	0	-	-
1.3	ENSRNOT00000022530	3	ENSRNOE00000159578	chr18:39598190-39598608	419	KCNN2_RAT	196-335	140	0	-	-
1.5	ENSRNOT00000022530	5	ENSRNOE00000159802	chr18:39671730-39671871	142	KCNN2_RAT	335-382	48	0	-	-
1.6	ENSRNOT00000022530	6	ENSRNOE00000160009	chr18:39689035-39689145	111	KCNN2_RAT	383-419	37	1	B:413-419	7
1.7	ENSRNOT00000022530	7	ENSRNOE00000160206	chr18:39696494-39696621	128	KCNN2_RAT	420-462	43	1	B:420-462	43
1.8	ENSRNOT00000022530	8	ENSRNOE00000160417	chr18:39702600-39702669	70	KCNN2_RAT	462-485	24	1	B:462-485	24
1.9	ENSRNOT00000022530	9	ENSRNOE00000160624	chr18:39704750-39705037	288	KCNN2_RAT	486-580	95	1	B:486-494 (gaps)	9

2.1	ENSRNOT00000022603	1	ENSRNOE00000444589	chr1:77252808-77252705	104	CALM3_RAT	1-1	1	0	-	-
2.2	ENSRNOT00000022603	2	ENSRNOE00000354112	chr1:77248702-77248672	31	CALM3_RAT	2-12	11	1	R:1-11	11
2.3	ENSRNOT00000022603	3	ENSRNOE00000337344	chr1:77246477-77246334	144	CALM3_RAT	12-60	49	1	R:11-59	49
2.4	ENSRNOT00000022603	4	ENSRNOE00000316778	chr1:77246246-77246140	107	CALM3_RAT	60-95	36	1	R:59-94	36
2.5	ENSRNOT00000022603	5	ENSRNOE00000294358	chr1:77246001-77245866	136	CALM3_RAT	96-141	46	1	R:95-140	46
2.6	ENSRNOT00000022603	6	ENSRNOE00000161097	chr1:77245776-77245475	302	CALM3_RAT	141-149	9	1	R:140-147	8
2.7	ENSRNOT00000022603	7	ENSRNOE00000437380	chr1:77244456-77244169	288	CALM3_RAT	-	0	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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain B from PDB  Type:PROTEIN  Length:81
 aligned with KCNN2_RAT | P70604 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:139
                                   422       432       442       452       462       472       482       492       502       512       522       532       542         
            KCNN2_RAT   413 DTQLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQNIMYDMISDLNERSEDFEKRIVTLETKLETLIGSIHALPGLISQTIRQQQRDFIETQMENYDKH 551
               SCOP domains d1g4yb_ B: Small-conductance potassium channel                                                                                              SCOP domains
               CATH domains 1g4yB00 B:413-494  [code=1.10.287.70, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------------------------------------------h..-..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.6    Exon 1.7  PDB: B:420-462 UniProt: 420-462  -----------------------Exon 1.9  PDB: B:486-494 (gaps) UniProt: 486-580 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.8  PDB: B:462-485------------------------------------------------------------------ Transcript 1 (2)
                 1g4y B 413 DTQLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAK---------------------------------------------------------TQL-HHHHH 494
                                   422       432       442       452       462       472       482  |      -         -         -         -         -         -| | |    
                                                                                                  485                                                       486 | |    
                                                                                                                                                              488 |    
                                                                                                                                                                490

Chain R from PDB  Type:PROTEIN  Length:147
 aligned with CALM1_RAT | P0DP29 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
            CALM1_RAT     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
               SCOP domains d1g4yr_ R: Calmodulin                                                                                                                               SCOP domains
               CATH domains 1g4yR01 R:1-80 EF-hand                                                          1g4yR02 R:81-143 EF-hand                                       ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhh......hhhhhhhhhhh.......eeehhhhhhhhh......hhhhhhhhhhhhh.....eeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------EF_HAND_2  PDB: R:7-42 UniProt: 8-43EF_HAND_2  PDB: R:43-78             -EF_HAND_2  PDB: R:80-115            EF_HAND_2  PDB: R:116-147        PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (5)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g4y R   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain R from PDB  Type:PROTEIN  Length:147
 aligned with CALM2_RAT | P0DP30 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
            CALM2_RAT     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
               SCOP domains d1g4yr_ R: Calmodulin                                                                                                                               SCOP domains
               CATH domains 1g4yR01 R:1-80 EF-hand                                                          1g4yR02 R:81-143 EF-hand                                       ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhh......hhhhhhhhhhh.......eeehhhhhhhhh......hhhhhhhhhhhhh.....eeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: R:7-42 UniProt: 8-43EF_HAND_2  PDB: R:43-78             -EF_HAND_2  PDB: R:80-115            EF_HAND_2  PDB: R:116-147        PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 1g4y R   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain R from PDB  Type:PROTEIN  Length:147
 aligned with CALM3_RAT | P0DP31 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
            CALM3_RAT     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
               SCOP domains d1g4yr_ R: Calmodulin                                                                                                                               SCOP domains
               CATH domains 1g4yR01 R:1-80 EF-hand                                                          1g4yR02 R:81-143 EF-hand                                       ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhh......hhhhhhhhhhh.......eeehhhhhhhhh......hhhhhhhhhhhhh.....eeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------EF_HAND_2  PDB: R:7-42 UniProt: 8-43EF_HAND_2  PDB: R:43-78             -EF_HAND_2  PDB: R:80-115            EF_HAND_2  PDB: R:116-147        PROSITE (3)
                PROSITE (4) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (4)
           Transcript 2 (1) Exon 2.2   -----------------------------------------------Exon 2.4  PDB: R:59-94              Exon 2.5  PDB: R:95-140 UniProt: 96-141       ------- Transcript 2 (1)
           Transcript 2 (2) ----------Exon 2.3  PDB: R:11-59 UniProt: 12-60            --------------------------------------------------------------------------------Exon 2.6 Transcript 2 (2)
                 1g4y R   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.70, no name defined] (106)

Norway rat (Rattus norvegicus) (4)

1g4yB00

B:413-494

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Norway rat (Rattus norvegicus) (37)

2a	1g4yR01	R:1-80
2b	1g4yR02	R:81-143

(no "Pfam Domain" information available for 1G4Y)

Asymmetric Unit(hide GO term definitions)

Chain B (KCNN2_RAT | P70604)

molecular function
	GO:0015269	calcium-activated potassium channel activity	Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient.
	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: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:0016286	small conductance calcium-activated potassium channel activity	Enables the transmembrane transfer of potassium by a channel with a unit conductance of 2 to 20 picoSiemens that opens in response to stimulus by internal calcium ions. Small conductance calcium-activated potassium channels are more sensitive to calcium than are large conductance calcium-activated potassium channels. Transport by a channel involves catalysis of facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism.
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:0048168	regulation of neuronal synaptic plasticity	A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
	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:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
	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:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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.

Chain R (CALM1_RAT | P0DP29)

Chain R (CALM3_RAT | P0DP31)

Chain R (CALM2_RAT | P0DP30)

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(no "Related Entries Specified in the PDB File" available for 1G4Y)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (9, 9)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (70, 72)

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