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(-) Description

Title :  STRUCTURE OF A BACTERIAL CYCLIC-NUCLEOTIDE REGULATED ION CHANNEL
 
Authors :  G. M. Clayton, J. M. Cabral-Morais
Date :  21 Nov 07  (Deposition) - 02 Dec 08  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transmembrane Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. Clayton, S. Altieri, L. Heginbotham, V. M. Unger, J. H. Morais-Cabral
Structure Of The Transmembrane Regions Of A Bacterial Cycli Nucleotide-Regulated Channel.
Proc. Natl. Acad. Sci. Usa V. 105 1511 2008
PubMed-ID: 18216238  |  Reference-DOI: 10.1073/PNAS.0711533105

(-) Compounds

Molecule 1 - MLL3241 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK
    Expression System Strain: BL21 (RP)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 381

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1K5Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:177 , TYR A:178 , K A:357 , GLY B:177 , TYR B:178 , TYR C:178 , TYR D:178BINDING SITE FOR RESIDUE K A 356
2AC2SOFTWARETHR A:175 , THR B:175 , THR C:175 , THR D:175BINDING SITE FOR RESIDUE K C 356
3AC3SOFTWARETHR A:176 , GLY A:177 , K A:356 , THR B:176 , GLY B:177 , THR C:176 , GLY C:177 , K C:357 , THR D:176 , GLY D:177BINDING SITE FOR RESIDUE K A 357
4AC4SOFTWARETHR A:175 , THR A:176 , K A:357 , THR B:175 , THR B:176 , THR C:175 , THR C:176 , THR D:175 , THR D:176BINDING SITE FOR RESIDUE K C 357

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZD9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZD9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZD9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CNGK1_RHILO235-348
 		  2B:235-239
C:235-239

(-) Exons   (0, 0)

(no "Exon" information available for 2ZD9)

(-) Sequences/Alignments

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:223
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:223
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
          CNGK1_RHILO    11 APLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAV 233
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zd9A01 A:11-125 Voltage-gated potassium channels                                                                  2zd9A02 A:126-233  [code=1.10.287.70, no name defined]                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zd9 A  11 APLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAV 233
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:231
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 
          CNGK1_RHILO     9 IYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAVPLFQKL 239
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zd9B01 B:9-125 Voltage-gated potassium channels                                                                     2zd9B02 B:126-239  [code=1.10.287.70, no name defined]                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CNMP_ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zd9 B   9 IYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAVPLFQKL 239
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 


Chain C from PDB  Type:PROTEIN  Length:234
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:234
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    
          CNGK1_RHILO     6 FLRIYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAVPLFQKL 239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2zd9C01 C:6-125 Voltage-gated potassium channels                                                                        2zd9C02 C:126-239  [code=1.10.287.70, no name defined]                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CNMP_ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zd9 C   6 FLRIYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAVPLFQKL 239
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    


Chain D from PDB  Type:PROTEIN  Length:225
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:225
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226     
          CNGK1_RHILO     7 LRIYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVA 231
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zd9D01 D:7-125 Voltage-gated potassium channels                                                                       2zd9D02 D:126-231  [code=1.10.287.70, no name defined]                                                     CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------Ion_trans_2-2zd9D01 D:133-216                                                       --------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------Ion_trans_2-2zd9D02 D:133-216                                                       --------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------Ion_trans_2-2zd9D03 D:133-216                                                       --------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------Ion_trans_2-2zd9D04 D:133-216                                                       --------------- Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zd9 D   7 LRIYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVA 231
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ZD9)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Ion_channel (150)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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  2zd9
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  CNGK1_RHILO | Q98GN8
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CNGK1_RHILO | Q98GN8: 1u12 1vp6 2k0g 2kxl 3beh 3cl1 3clp 3co2 4chv 4chw 4muv

(-) Related Entries Specified in the PDB File

3beh LOW CYCLIC-AMP