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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF THE HUMAN CHLORIDE CHANNEL CLC-KA

Authors :   S. Markovic, R. Dutzler

Date :   05 Apr 07 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Cystathionine Beta Synthetase (Cbs) Domains Containing Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Markovic, R. Dutzler
The Structure Of The Cytoplasmic Domain Of The Chloride Channel Clc-Ka Reveals A Conserved Interaction Interface.
Structure V. 15 715 2007
PubMed-ID: 17562318 | Reference-DOI: 10.1016/J.STR.2007.04.013
(for further references see the PDB file header)

Molecule 1 - CHLORIDE CHANNEL PROTEIN CLC-KA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET 28B+
	Expression System Strain	:	BL21/DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	HUMAN CLC-KA C-TERMINAL DOMAIN
	Gene	:	CLCNKA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CHLORIDE CHANNEL KA, CLC-K1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	IOD	1	Ligand/Ion	IODIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:687	BINDING SITE FOR RESIDUE IOD A 501
2	AC2	SOFTWARE	TRP B:670 , ILE B:677	BINDING SITE FOR RESIDUE CL B 503

(no "SS Bond" information available for 2PFI)

(no "Cis Peptide Bond" information available for 2PFI)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061095	P	683	L	CLCKA_HUMAN	Polymorphism	12746751	A/B	P	683	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CBS	PS51371	CBS domain profile.	CLCKA_HUMAN	551-609 626-684	4	A:551-605 B:551-608 A:626-684 B:626-684

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.6d	ENST00000331433	6d	ENSE00001932203	chr1:16348547-16348558	12	CLCKA_HUMAN	-	0	0	-	-
1.7	ENST00000331433	7	ENSE00002142746	chr1:16349108-16349214	107	CLCKA_HUMAN	1-34	34	0	-	-
1.8	ENST00000331433	8	ENSE00001792243	chr1:16350295-16350423	129	CLCKA_HUMAN	34-77	44	0	-	-
1.9a	ENST00000331433	9a	ENSE00001687047	chr1:16351258-16351386	129	CLCKA_HUMAN	77-120	44	0	-	-
1.10a	ENST00000331433	10a	ENSE00001318549	chr1:16352603-16352742	140	CLCKA_HUMAN	120-166	47	0	-	-
1.11b	ENST00000331433	11b	ENSE00001677163	chr1:16353031-16353108	78	CLCKA_HUMAN	167-192	26	0	-	-
1.12	ENST00000331433	12	ENSE00001670784	chr1:16353192-16353270	79	CLCKA_HUMAN	193-219	27	0	-	-
1.14	ENST00000331433	14	ENSE00001698312	chr1:16353805-16353930	126	CLCKA_HUMAN	219-261	43	0	-	-
1.15	ENST00000331433	15	ENSE00001766047	chr1:16354316-16354400	85	CLCKA_HUMAN	261-289	29	0	-	-
1.16	ENST00000331433	16	ENSE00001302130	chr1:16354513-16354614	102	CLCKA_HUMAN	289-323	35	0	-	-
1.17b	ENST00000331433	17b	ENSE00001759246	chr1:16355256-16355340	85	CLCKA_HUMAN	323-351	29	0	-	-
1.18	ENST00000331433	18	ENSE00001714023	chr1:16355621-16355794	174	CLCKA_HUMAN	352-409	58	0	-	-
1.19	ENST00000331433	19	ENSE00001612488	chr1:16356226-16356295	70	CLCKA_HUMAN	410-433	24	0	-	-
1.20	ENST00000331433	20	ENSE00001676808	chr1:16356460-16356570	111	CLCKA_HUMAN	433-470	38	0	-	-
1.21	ENST00000331433	21	ENSE00001766307	chr1:16356956-16357169	214	CLCKA_HUMAN	470-541	72	0	-	-
1.22	ENST00000331433	22	ENSE00001293563	chr1:16358205-16358338	134	CLCKA_HUMAN	541-586	46	2	A:542-586 B:542-586	45 45
1.23	ENST00000331433	23	ENSE00001617962	chr1:16358698-16358786	89	CLCKA_HUMAN	586-615	30	2	A:586-615 (gaps) B:586-615 (gaps)	30 30
1.24a	ENST00000331433	24a	ENSE00001718331	chr1:16358938-16359021	84	CLCKA_HUMAN	616-643	28	2	A:616-643 B:616-643	28 28
1.25	ENST00000331433	25	ENSE00001784874	chr1:16359665-16359751	87	CLCKA_HUMAN	644-672	29	2	A:644-672 B:644-672	29 29
1.26b	ENST00000331433	26b	ENSE00001800918	chr1:16360106-16360545	440	CLCKA_HUMAN	673-687	15	2	A:673-687 B:673-687	15 15

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
	(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:145
 aligned with CLCKA_HUMAN | P51800 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:152
                                                                                                                                                                           687      
                                   551       561       571       581       591       601       611       621       631       641       651       661       671       681     |   -  
          CLCKA_HUMAN   542 SHHVRVEHFMNHSITTLAKDTPLEEVVKVVTSTDVTEYPLVESTESQILVGIVQRAQLVQALQAEPPSRAPGHQQCLQDILARGCPTEPVTLTLFSETTLHQAQNLFKLLNLQSLFVTSRGRAVGCVSWVEMKKAISNLTNPPAPK------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh......ee...hhhhhhhhhhh....eeeee.......eeeeeehhhhhhhhhh-------....hhhhhhhh..........ee...hhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------L---------- SAPs(SNPs)
                    PROSITE ---------CBS  PDB: A:551-605 UniProt: 551-609                       ----------------CBS  PDB: A:626-684 UniProt: 626-684                       --------- PROSITE
           Transcript 1 (1) Exon 1.22  PDB: A:542-586 UniProt: 541-586   -----------------------------Exon 1.24a  PDB: A:616-643  Exon 1.25  PDB: A:644-672    Exon 1.26b     ------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.23 UniProt: 586-615    ------------------------------------------------------------------------------ Transcript 1 (2)
                 2pfi A 542 SHHVRVEHFMNHSITTLAKDTPLEEVVKVVTSTDVTEYPLVESTESQILVGIVQRAQLVQALQA-------GHQQCLQDILARGCPTEPVTLTLFSETTLHQAQNLFKLLNLQSLFVTSRGRAVGCVSWVEMKKAISNLTNPPAPKEFLEVL 693
                                   551       561       571       581       591       601   |     - |     621       631       641       651       661       671       681       691  
                                                                                         605     613

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with CLCKA_HUMAN | P51800 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:152
                                                                                                                                                                           687      
                                   551       561       571       581       591       601       611       621       631       641       651       661       671       681     |   -  
          CLCKA_HUMAN   542 SHHVRVEHFMNHSITTLAKDTPLEEVVKVVTSTDVTEYPLVESTESQILVGIVQRAQLVQALQAEPPSRAPGHQQCLQDILARGCPTEPVTLTLFSETTLHQAQNLFKLLNLQSLFVTSRGRAVGCVSWVEMKKAISNLTNPPAPK------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------CBS-2pfiB01 B:623-679                                    -------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------CBS-2pfiB02 B:623-679                                    -------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------CBS-2pfiB03 B:623-679                                    -------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------CBS-2pfiB04 B:623-679                                    -------------- Pfam domains (4)
         Sec.struct. author ....hhhhhh......ee...hhhhhhhhhh.....eeeee.......eeeeeehhhhhhhhhhh..----....hhhhhhhhh.........ee...hhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------L---------- SAPs(SNPs)
                    PROSITE ---------CBS  PDB: B:551-608 UniProt: 551-609                       ----------------CBS  PDB: B:626-684 UniProt: 626-684                       --------- PROSITE
           Transcript 1 (1) Exon 1.22  PDB: B:542-586 UniProt: 541-586   -----------------------------Exon 1.24a  PDB: B:616-643  Exon 1.25  PDB: B:644-672    Exon 1.26b     ------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.23 UniProt: 586-615    ------------------------------------------------------------------------------ Transcript 1 (2)
                 2pfi B 542 SHHVRVEHFMNHSITTLAKDTPLEEVVKVVTSTDVTEYPLVESTESQILVGIVQRAQLVQALQAEPP----GHQQCLQDILARGCPTEPVTLTLFSETTLHQAQNLFKLLNLQSLFVTSRGRAVGCVSWVEMKKAISNLTNPPAPKEFLEVL 693
                                   551       561       571       581       591       601      |  - |     621       631       641       651       661       671       681       691  
                                                                                            608  613

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 2PFI)

(no "CATH Domain" information available for 2PFI)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CBS] (51)

Family: CBS (51)

Homo sapiens (Human) (7)

1a	CBS-2pfiB01	B:623-679
1b	CBS-2pfiB02	B:623-679
1c	CBS-2pfiB03	B:623-679
1d	CBS-2pfiB04	B:623-679

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CLCKA_HUMAN | P51800)

molecular function
	GO:0005254	chloride channel activity	Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005247	voltage-gated chloride channel activity	Enables the transmembrane transfer of a chloride 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.
	GO:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. 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:1902476	chloride transmembrane transport	The directed movement of chloride across a membrane.
	GO:0006821	chloride transport	The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007588	excretion	The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
	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:1903959	regulation of anion transmembrane transport	Any process that modulates the frequency, rate or extent of anion transmembrane transport.
	GO:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	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:0034707	chloride channel complex	An ion channel complex through which chloride ions pass.
	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.
	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.

Asymmetric/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (5, 10)

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