3F7Y - JenaLib

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Title :   KCSA POTASSIUM CHANNEL IN THE PARTIALLY OPEN STATE WITH 17 A OPENING AT T112

Authors :   L. G. Cuello, V. Jogini, D. M. Cortes, E. Perozo

Date :   10 Nov 08 (Deposition) - 19 May 10 (Release) - 09 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,B,C  (4x)

Keywords :   Kcsa, Open, Inactivation, Potassium Channel, Cell Membrane, Ion Transport, Ionic Channel, Membrane, Transmembrane, Transport, Voltage-Gated Channel, Membrane Protein-Metal Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. G. Cuello, V. Jogini, D. M. Cortes, E. Perozo
Kcsa Potassium Channel In The Partially Open State With 17 Opening At T112
To Be Published
PubMed: search

Molecule 1 - ANTIBODY FAB FRAGMENT HEAVY CHAIN
	Chains	:	A
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTIBODY FAB FRAGMENT LIGHT CHAIN
	Chains	:	B
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - VOLTAGE-GATED POTASSIUM CHANNEL
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	XL10-GOLD
	Expression System Taxid	:	562
	Expression System Vector	:	PQE70
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 21-124
	Gene	:	KCSA, SKC1
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES LIVIDANS
	Organism Taxid	:	1916

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	K C:2 , THR C:75	BINDING SITE FOR RESIDUE K C 1
2	AC2	SOFTWARE	K C:1 , THR C:75 , VAL C:76	BINDING SITE FOR RESIDUE K C 2
3	AC3	SOFTWARE	GLY C:77 , TYR C:78	BINDING SITE FOR RESIDUE K C 3

Asymmetric Unit

No.	Residues
1	A:22	-	A:96
2	B:23	-	B:88
3	B:134	-	B:194

Asymmetric Unit

No.	Residues
1	Phe A:151	-	Pro A:152
2	Glu A:153	-	Pro A:154
3	Trp A:193	-	Pro A:194
4	Ser B:7	-	Pro B:8
5	Trp B:94	-	Pro B:95
6	Tyr B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 3F7Y)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	B:192-198

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	B:192-198

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	4	B:192-198

(no "Exon" information available for 3F7Y)

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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f7yA01 A:1-118 Immunoglobulins                                                                                       3f7yA02 A:119-217 Immunoglobulins                                                                  -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f7y A   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANYNEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                        1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102  
           IGKC_MOUSE     - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 104
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3f7yB02 B:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f7y B   1 DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with KCSA_STRLI | P0A334 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:88
                                    36        46        56        66        76        86        96       106        
           KCSA_STRLI    27 RAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWF 114
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f7yC00 C:27-114  [code=1.10.287.70, no name defined]                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3f7y C  27 RAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWF 114
                                    36        46        56        66        76        86        96       106

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 3F7Y)

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)

Mus musculus. Organism_taxid: 10090. Mus musculus. Organism_taxid: 10090. (8)

3f7yC00

C:27-114

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mus musculus. Organism_taxid: 10090. Mus musculus. Organism_taxid: 10090. (10)

2a	3f7yB02	B:109-211
2b	3f7yA02	A:119-217
2c	3f7yA01	A:1-118

(no "Pfam Domain" information available for 3F7Y)

Asymmetric Unit(hide GO term definitions)

Chain B (IGKC_MOUSE | P01837)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	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 C (KCSA_STRLI | P0A334)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.

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	Cis Peptide Bonds
		Glu A:153 - Pro A:154	[ RasMol ]
		Phe A:151 - Pro A:152	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Trp A:193 - Pro A:194	[ RasMol ]
		Trp B:94 - Pro B:95	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]

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	3f7y
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	KCSA_STRLI \| P0A334
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3f5w	KCSA POTASSIUM CHANNEL IN THE OPEN-INACTIVATED STATE WITH 32 A OPENING AT T112
3f7v	KCSA POTASSIUM CHANNEL IN THE OPEN-INACTIVATED STATE WITH 23 A OPENING AT T112
3fb5	KCSA POTASSIUM CHANNEL IN THE PARTIALLY OPEN STATE WITH 14.5 A OPENING AT T112
3fb6	KCSA POTASSIUM CHANNEL IN THE PARTIALLY OPEN STATE WITH 16 A OPENING AT T112
3fb7	OPEN KCSA POTASSIUM CHANNEL IN THE PRESENCE OF RB+ ION
3fb8	KCSA POTASSIUM CHANNEL IN THE OPEN-CONDUCTIVE STATE WITH 20 A OPENING AT T112 IN THE PRESENCE OF RB+ ION

Description

Compounds

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Ligands, Modified Residues, Ions (1, 4)

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SS Bonds (3, 3)

Cis Peptide Bonds (6, 6)

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Gene Ontology (23, 24)

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