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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MTHK RCK IN COMPLEX WITH CADMIUM
 
Authors :  H. Dvir, S. Choe
Date :  02 Dec 09  (Deposition) - 21 Apr 10  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rck, Mthk, Cadmium, Potassium Channel, Alternative Initiation, Ion Transport, Ionic Channel, Membrane, Metal-Binding, Potassium, Potassium Transport, Transmembrane, Transport, Cell Membrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Dvir, E. Valera, S. Choe
Structure Of The Mthk Rck In Complex With Cadmium.
J. Struct. Biol. V. 171 231 2010
PubMed-ID: 20371380  |  Reference-DOI: 10.1016/J.JSB.2010.03.020

(-) Compounds

Molecule 1 - CALCIUM-GATED POTASSIUM CHANNEL MTHK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RCK DOMAIN
    Gene: MTHK, MTH_1520
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS STR. DELTA H
    Organism Taxid: 187420
    Synonym: MTHK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:47 , ASP B:184 , GLU B:210BINDING SITE FOR RESIDUE CD B 601
2AC2SOFTWAREASP A:184 , GLU A:210 , GLU A:212BINDING SITE FOR RESIDUE CD A 602
3AC3SOFTWAREGLU A:144 , HIS A:161BINDING SITE FOR RESIDUE CD A 603
4AC4SOFTWAREARG A:262 , GLY A:290 , GLU A:326 , ASP B:305BINDING SITE FOR RESIDUE CD A 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KXD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KXD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RCK_NPS51201 RCK N-terminal domain profile.MTHK_METTH117-237
 		  2A:117-237
B:117-237
2RCK_CPS51202 RCK C-terminal domain profile.MTHK_METTH252-336
 		  2A:252-336
B:252-334

(-) Exons   (0, 0)

(no "Exon" information available for 3KXD)

(-) 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:224
 aligned with MTHK_METTH | O27564 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:224
                                                                                                                                                                                                                                                      336   
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335|   
           MTHK_METTH   116 RHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISA---   -
               SCOP domains d3kxda1 A:116-244 automated matches                                                                                              d3kxda2 A:245-339 automated matches                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhh....eeeee.hhhhhhhhhhh..eeee....hhhhhhhh......eeee...hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhhhhhhhhhh...hhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh.eeeeeee..eeee............eeeeeehhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RCK_N  PDB: A:117-237 UniProt: 117-237                                                                                   --------------RCK_C  PDB: A:252-336 UniProt: 252-336                                               --- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxd A 116 RHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISALVP 339
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with MTHK_METTH | O27564 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:219
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325         
           MTHK_METTH   116 RHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYI 334
               SCOP domains d3kxdb1 B:116-244 automated matches                                                                                              d3kxdb2 B:245-334 automated matches                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --TrkA_N-3kxdB01 B:118-231                                                                                          --------------------------------TrkA_C-3kxdB03 B:264-334                                                Pfam domains (1)
           Pfam domains (2) --TrkA_N-3kxdB02 B:118-231                                                                                          --------------------------------TrkA_C-3kxdB04 B:264-334                                                Pfam domains (2)
         Sec.struct. author ..eeee..hhhhhhhhhhh....eeeee.hhhhhhhhhhh..eeee....hhhhhhhh......eeee...hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhh......eeeeee..........hhhhhhhhhhhh.eeeeeee..eeee............eeeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RCK_N  PDB: B:117-237 UniProt: 117-237                                                                                   --------------RCK_C  PDB: B:252-334 UniProt: 252-336                                              PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxd B 116 RHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYI 334
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KXD)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: TrkA_C] (4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MTHK_METTH | O27564)
molecular function
    GO:0008324    cation transmembrane transporter activity    Enables the transfer of cation from one side of the membrane to the other.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0098655    cation transmembrane transport    A process in which a cation 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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTHK_METTH | O27564: 1lnq 2aef 2aej 2aem 2fy8 2ogu 3ldc 3ldd 3lde 3ous 3r65 3rbx 3rbz 4ei2 4hyo 4hz3 4l73 4l74 4l75 4l76 4qe7 4qe9 4ro0

(-) Related Entries Specified in the PDB File

2aef 2aej