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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC COILED-COIL (I/I-TYPE) ASSEMBLY DOMAIN FROM THE VOLTAGE-GATED PROTON CHANNEL MUTANT
 
Authors :  Y. Fujiwara, K. Takeshita, A. Nakagawa
Date :  25 Sep 12  (Deposition) - 27 Feb 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Biol. Unit 4:  J,K,L  (1x)
Keywords :  Coiled-Coil, Assembly, Cytoplasmic, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fujiwara, T. Kurokawa, K. Takeshita, A. Nakagawa, H. P. Larsson, Y. Okamura
Gating Of The Designed Trimeric/Tetrameric Voltage-Gated H+ Channel.
J. Physiol. (Paris) V. 591 627 2013
PubMed-ID: 23165764  |  Reference-DOI: 10.1113/JPHYSIOL.2012.243006

(-) Compounds

Molecule 1 - VOLTAGE-GATED HYDROGEN CHANNEL 1
    Chains: A, B, D, C, E, F, H, G, I, J, K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 220-269
    Gene: HVCN1, BTS, VSOP
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HYDROGEN VOLTAGE-GATED CHANNEL 1, HV1, VOLTAGE SENSOR DOMAIN-ONLY PROTEIN, MVSOP

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABC         
Biological Unit 2 (1x):    DEF      
Biological Unit 3 (1x):       GHI   
Biological Unit 4 (1x):          JKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3VYI)

(-) Sites  (0, 0)

(no "Site" information available for 3VYI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VYI)

(-) Exons   (0, 0)

(no "Exon" information available for 3VYI)

(-) Sequences/Alignments

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:46
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:46
                                   229       239       249       259      
          HVCN1_MOUSE   220 SERQILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLKQNGLL 265
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 3vyi A 220 SERQILRIKQNINQIATKIQHIEFSISEIEQEIERINKLIKQNGLL 265
                                   229       239       249       259      


Chain B from PDB  Type:PROTEIN  Length:46
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:46
                                   229       239       249       259      
          HVCN1_MOUSE   220 SERQILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLKQNGLL 265
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 3vyi B 220 SERQILRIKQNINQIATKIQHIEFSISEIEQEIERINKLIKQNGLL 265
                                   229       239       249       259      


Chain C from PDB  Type:PROTEIN  Length:48
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:48
                                   229       239       249       259        
          HVCN1_MOUSE   220 SERQILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLKQNGLLGD 267
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 3vyi C 220 SERQILRIKQNINQIATKIQHIEFSISEIEQEIERINKLIKQNGLLGD 267
                                   229       239       249       259        


Chain D from PDB  Type:PROTEIN  Length:48
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:48
                                   228       238       248       258        
          HVCN1_MOUSE   219 RSERQILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLKQNGLLG 266
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 3vyi D 219 GSERQILRIKQNINQIATKIQHIEFSISEIEQEIERINKLIKQNGLLG 266
                                   228       238       248       258        


Chain E from PDB  Type:PROTEIN  Length:46
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:46
                                   229       239       249       259      
          HVCN1_MOUSE   220 SERQILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLKQNGLL 265
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 3vyi E 220 SERQILRIKQNINQIATKIQHIEFSISEIEQEIERINKLIKQNGLL 265
                                   229       239       249       259      


Chain F from PDB  Type:PROTEIN  Length:49
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:49
                                   228       238       248       258         
          HVCN1_MOUSE   219 RSERQILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLKQNGLLGD 267
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3vyi F 219 GSERQILRIKQNINQIATKIQHIEFSISEIEQEIERINKLIKQNGLLGD 267
                                   228       238       248       258         


Chain G from PDB  Type:PROTEIN  Length:40
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:41
                                     230                             
                                   229 |                             
                                   229 |     238       248       258 
          HVCN1_MOUSE   220 SERQILRLKQ-INIQLATKIQHLEFSCSEKEQEIERLNKLL 259
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh-hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3vyi G 220 SERQILRIKQNIN-QIATKIQHIEFSISEIEQEIERINKLI 259
                                   229  | |  238       248       258 
                                      232 |                          
                                        233                          


Chain H from PDB  Type:PROTEIN  Length:40
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:41
                                    230                              
                                  229 |                              
                                    |-|      239       249       259 
          HVCN1_MOUSE   221 ERQILRLKQ-INIQLATKIQHLEFSCSEKEQEIERLNKLLK 260
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh-hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3vyi H 221 ERQILRIKQNIN-QIATKIQHIEFSISEIEQEIERINKLIK 260
                                   230 | |   239       249       259 
                                     232 |                           
                                       233                           


Chain I from PDB  Type:PROTEIN  Length:40
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:41
                                     230                             
                                   229 |                             
                                   229 |     238       248       258 
          HVCN1_MOUSE   220 SERQILRLKQ-INIQLATKIQHLEFSCSEKEQEIERLNKLL 259
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh-hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3vyi I 220 SERQILRIKQNIN-QIATKIQHIEFSISEIEQEIERINKLI 259
                                   229  | |  238       248       258 
                                      232 |                          
                                        233                          


Chain J from PDB  Type:PROTEIN  Length:42
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:43
                                     230                               
                                   229 |                               
                                   229 |     238       248       258   
          HVCN1_MOUSE   220 SERQILRLKQ-INIQLATKIQHLEFSCSEKEQEIERLNKLLKQ 261
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh-hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 3vyi J 220 SERQILRIKQNIN-QIATKIQHIEFSISEIEQEIERINKLIKQ 261
                                   229  | |  238       248       258   
                                      232 |                            
                                        233                            


Chain K from PDB  Type:PROTEIN  Length:39
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:40
                                   230                              
                                 229 |                              
                                   230       240       250       260
          HVCN1_MOUSE   222 RQILRLKQ-INIQLATKIQHLEFSCSEKEQEIERLNKLLK 260
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh-hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3vyi K 222 RQILRIKQNIN-QIATKIQHIEFSISEIEQEIERINKLIK 260
                                   231| |    240       250       260
                                    232 |                           
                                      233                           


Chain L from PDB  Type:PROTEIN  Length:38
 aligned with HVCN1_MOUSE | Q3U2S8 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:39
                                    230                            
                                  229 |                            
                                    |-|      239       249         
          HVCN1_MOUSE   221 ERQILRLKQ-INIQLATKIQHLEFSCSEKEQEIERLNKL 258
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh-hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3vyi L 221 ERQILRIKQNIN-QIATKIQHIEFSISEIEQEIERINKL 258
                                   230 | |   239       249         
                                     232 |                         
                                       233
   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 3VYI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L   (HVCN1_MOUSE | Q3U2S8)
molecular function
    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: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.
    GO:0030171    voltage-gated proton channel activity    Enables the transmembrane transfer of a proton 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:0071467    cellular response to pH    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0071294    cellular response to zinc ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
    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:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0009268    response to pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0010043    response to zinc ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HVCN1_MOUSE | Q3U2S8: 3vmx 3vmy 3vmz 3vn0 3wkv

(-) Related Entries Specified in the PDB File

3vmx 3vmy 3vmz 3vn0